[WIP] Rhar768/feature/23 rest interface

.github/ISSUE_TEMPLATE/documentation.md

@@ -0,0 +1,17 @@
+---
+name: Documentation
+about: Create a report to help us improve
+title: ''
+labels: documentation
+assignees: ''
+
+---
+### User Story: 
+
+As a \<type of user\>, I want \<some feature\> so that \<some reason\>
+
+
+### Acceptance Criteria:
+
+1) 
+2)

.github/ISSUE_TEMPLATE/epic.md

@@ -0,0 +1,26 @@
+---
+name: UoA Epic
+about: Create an epic
+title: ''
+labels: epic
+assignees: ''
+
+---
+
+**Epic**
+<!--As a [user role], I'd like to [do something], so that [some goal].-->
+
+**Acceptance Criteria**
+
+- 
+-
+
+**User Stories**
+
+-
+-
+
+**Notes**
+
+---
+

.github/ISSUE_TEMPLATE/feature-request-uoa.md

@@ -0,0 +1,28 @@
+---
+name: UoA Feature Request
+about: Create a feature request
+title: ''
+labels: user story
+assignees: ''
+
+---
+
+<!--Please start the issue title with [Xpt] where X is the number of story points estimated for the issue.-->
+
+**User Story**
+<!--As a [user role], I'd like to [do something], so that [some goal].-->
+
+**Acceptance Criteria**
+
+- 
+-
+
+**Notes**
+
+---
+
+**Why is this feature needed? Please describe the problem your requested feature wants to solve**
+<!-- Describe what the problem is. Ex. I'm always frustrated when ... -->
+
+**Describe the solution you'd like**
+<!--Describe what you want to happen -->

build.gradle

@@ -184,7 +184,7 @@ dependencies {
 
     implementation group: 'jakarta.activation', name: 'jakarta.activation-api', version: '1.2.1'
     implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '2.3.2'
-    implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '2.3.2'
+    implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '2.3.3'
 
     implementation ('com.github.tomtung:latex2unicode_2.12:0.2.6') {
         exclude module: 'fastparse_2.12'
@@ -199,6 +199,21 @@ dependencies {
     implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.62.2'
     implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.62.2'
 
+    // Required for the standalone server
+    implementation 'javax.servlet:javax.servlet-api:4.0.1'
+    implementation 'org.eclipse.jetty:jetty-servlet:9.4.31.v20200723'
+    implementation 'org.eclipse.jetty:jetty-servlets:9.4.31.v20200723'
+    implementation 'org.glassfish.jersey.containers:jersey-container-servlet:2.31'
+    implementation 'org.glassfish.jersey.inject:jersey-hk2:2.31'
+    //implementation 'org.glassfish.jersey.bundles:jaxrs-ri:2.31'
+
+    // Required to serialize and deserialize data at the http API
+    //implementation 'org.glassfish.jersey.media:jersey-media-json-jackson:2.31'
+    implementation 'org.glassfish.jersey.core:jersey-common:2.31'
+    //implementation 'com.fasterxml.jackson.core:jackson-core:2.11.2'
+    //implementation 'com.fasterxml.jackson.core:jackson-databind:2.11.2'
+    //implementation 'com.fasterxml.jackson.core:jackson-annotations:2.11.2'
+
     testImplementation 'io.github.classgraph:classgraph:4.8.89'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.6.2'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.6.2'

src/main/java/module-info.java

@@ -91,4 +91,8 @@
     requires com.h2database.mvstore;
     requires lucene.queryparser;
     requires lucene.core;
+    requires org.eclipse.jetty.server;
+    requires org.eclipse.jetty.servlet;
+    requires jersey.container.servlet.core;
+    requires java.ws.rs;
 }

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

@@ -95,6 +95,7 @@
 import org.jabref.gui.importer.actions.OpenDatabaseAction;
 import org.jabref.gui.importer.fetcher.LookupIdentifierAction;
 import org.jabref.gui.integrity.IntegrityCheckAction;
+import org.jabref.gui.jabmap.JabMapAction;
 import org.jabref.gui.journals.AbbreviateAction;
 import org.jabref.gui.journals.ManageJournalsAction;
 import org.jabref.gui.keyboard.CustomizeKeyBindingAction;
@@ -869,7 +870,11 @@ private MenuBar createMenu() {
                 new SeparatorMenuItem(),
 
                 factory.createMenuItem(StandardActions.SEND_AS_EMAIL, new SendAsEMailAction(dialogService, stateManager)),
-                pushToApplicationMenuItem
+                pushToApplicationMenuItem,
+
+                new SeparatorMenuItem(),
+
+                factory.createMenuItem(StandardActions.LAUNCH_JABMAP, new JabMapAction(this))
         );
 
         SidePaneComponent webSearch = sidePaneManager.getComponent(SidePaneType.WEB_SEARCH);

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

@@ -1,12 +1,13 @@
 package org.jabref.gui;
 
-import java.net.Authenticator;
-
 import javafx.application.Application;
 import javafx.application.Platform;
 import javafx.scene.control.Alert;
 import javafx.stage.Stage;
-
+import org.apache.commons.cli.ParseException;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletContextHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
 import org.jabref.cli.ArgumentProcessor;
 import org.jabref.cli.JabRefCLI;
 import org.jabref.gui.remote.JabRefMessageHandler;
@@ -25,11 +26,12 @@
 import org.jabref.migrations.PreferencesMigrations;
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.preferences.JabRefPreferences;
-
-import org.apache.commons.cli.ParseException;
+import org.jabref.rest.resources.RootResource;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.net.Authenticator;
+
 /**
  * JabRef's main class to process command line options and to start the UI
  */
@@ -72,7 +74,15 @@ public void start(Stage mainStage) {
                     return;
                 }
 
-                // If not, start GUI
+                startHttpEndPoint();
+
+                // TODO: How and when to shut down the server
+                // Waits until server is finished.
+                // Will never happen, thus user has to press Ctrl+C.
+                // See also https://stackoverflow.com/a/14981621/873282.
+                // server.join();
+
+                // If there isn't a running JabRef instance or multiple instances are allowed, start GUI
                 new JabRefGUI(mainStage, argumentProcessor.getParserResults(), argumentProcessor.isBlank());
             } catch (ParseException e) {
                 LOGGER.error("Problem parsing arguments", e);
@@ -86,6 +96,39 @@ public void start(Stage mainStage) {
         }
     }
 
+    private void startHttpEndPoint() {
+        Server server = this.createHttpServer();
+        //Starts server to http://localhost:9898/libraries/current/entries
+
+        try {
+            server.start();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
+
+    private Server createHttpServer() {
+        ServletContextHandler context = new ServletContextHandler(ServletContextHandler.SESSIONS);
+        context.setContextPath("/");
+
+        Server server = new Server(9898);
+        server.setHandler(context);
+        this.addServlet(context);
+        return server;
+    }
+
+    private void addServlet(ServletContextHandler context) {
+        // this mirrors a webapp/WEB-INF/web.xml
+        ServletHolder jerseyServlet = context.addServlet(
+                org.glassfish.jersey.servlet.ServletContainer.class, "/*");
+        jerseyServlet.setInitOrder(0);
+
+        // Tells the Jersey Servlet which REST service/class to load.
+        jerseyServlet.setInitParameter(
+                "jersey.config.server.provider.classnames",
+                RootResource.class.getCanonicalName());
+    }
+
     @Override
     public void stop() {
         Globals.stopBackgroundTasks();

src/main/java/org/jabref/gui/actions/StandardActions.java

@@ -9,6 +9,7 @@
 
 public enum StandardActions implements Action {
 
+    LAUNCH_JABMAP(Localization.lang("Launch JabMap"), IconTheme.JabRefIcons.BOOK, KeyBinding.LAUNCH_JABMAP),
     COPY_MORE(Localization.lang("Copy") + "..."),
     COPY_TITLE(Localization.lang("Copy title"), KeyBinding.COPY_TITLE),
     COPY_KEY(Localization.lang("Copy citation key"), KeyBinding.COPY_CITATION_KEY),

src/main/java/org/jabref/gui/jabmap/JabMapAction.java

@@ -0,0 +1,20 @@
+package org.jabref.gui.jabmap;
+
+import org.jabref.gui.JabRefFrame;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.logic.jabmap.MindMapWriter;
+
+
+public class JabMapAction extends SimpleCommand {
+
+    JabRefFrame jabRefFrame;
+
+    public JabMapAction(JabRefFrame jabRefFrame) {
+        this.jabRefFrame = jabRefFrame;
+    }
+
+    @Override
+    public void execute() {
+        new MindMapWriter(jabRefFrame);
+    }
+}

src/main/java/org/jabref/gui/keyboard/KeyBinding.java

@@ -42,6 +42,7 @@ public enum KeyBinding {
     HELP("Help", Localization.lang("Help"), "F1", KeyBindingCategory.FILE),
     IMPORT_INTO_CURRENT_DATABASE("Import into current library", Localization.lang("Import into current library"), "ctrl+I", KeyBindingCategory.FILE),
     IMPORT_INTO_NEW_DATABASE("Import into new library", Localization.lang("Import into new library"), "ctrl+alt+I", KeyBindingCategory.FILE),
+    LAUNCH_JABMAP("Launch JabMap", Localization.lang("Launch JabMap"), "ctrl+j", KeyBindingCategory.TOOLS),
     NEW_ARTICLE("New article", Localization.lang("New article"), "ctrl+shift+A", KeyBindingCategory.BIBTEX),
     NEW_BOOK("New book", Localization.lang("New book"), "ctrl+shift+B", KeyBindingCategory.BIBTEX),
     NEW_ENTRY("New entry", Localization.lang("New entry"), "ctrl+N", KeyBindingCategory.BIBTEX),

src/main/java/org/jabref/logic/jabmap/BibtexMindMapAdapter.java

@@ -0,0 +1,108 @@
+package org.jabref.logic.jabmap;
+
+import javafx.collections.ObservableList;
+import org.jabref.model.database.BibDatabase;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.field.Field;
+import org.jabref.model.jabmap.EdgeDirection;
+import org.jabref.model.jabmap.MindMap;
+import org.jabref.model.jabmap.MindMapEdge;
+import org.jabref.model.jabmap.MindMapNode;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+
+import static org.jabref.model.jabmap.MindMapEdge.*;
+import static org.jabref.model.jabmap.MindMapNode.*;
+
+/**
+ * This class handles converting data from BibTeX format, which is stored in the database, to MindMap to be sent to JapMap
+ * It also does the reverse, converting JSON to BibTeX to be stored.
+ */
+public class BibtexMindMapAdapter {
+
+    public static final String DEFAULT_MAP_NAME = "New Map";
+
+    /**
+     * Method for loading MindMap class from bibtex file. Returns the mindmap object if present, a blank map otherwise
+     */
+    public MindMap bibtex2MindMap(BibDatabase database) {
+        ObservableList<BibEntry> observableList = database.getEntries();
+        // TODO: Where to handle/generate node & edge citation keys, which JabRef needs to read into database
+        // Retrieve map, nodes, and edges from list of bib entries
+        Optional<BibEntry> optionalMapEntry = observableList.stream().filter(o -> o.getType().getDisplayName().equals("Mapnode")).findFirst();
+        if (optionalMapEntry.isPresent()) {
+            // We know this file contains a mind map so...
+            MindMap map = new MindMap();
+            try {
+                for (BibEntry b : observableList) {
+                    switch (b.getType().getDisplayName()) {
+                        case MAP_NODE_ENTRY_NAME -> {
+                            // Instantiate MindMapNode object and add to MindMap nodes
+                            map.addNode(createNodeFromBibEntry(b));
+                        }
+                        case MAP_EDGE_ENTRY_NAME -> {
+                            // Instantiate MindMapEdge object and add to MindMap edges
+                            map.addEdge(createEdgeFromBibEntry(b));
+                        }
+                    }
+                }
+                return map;
+            } catch (IllegalArgumentException e) {
+                System.out.println("Error parsing map from bibtex, returning clean one instead");
+            }
+        }
+        //Return blank mind map
+        MindMap newMap = new MindMap();
+        newMap.addNode(new MindMapNode(DEFAULT_MAP_NAME));
+        return newMap;
+    }
+
+    /**
+     * Method to convert MindMap class to bibtex entries that can then be saved in the database
+     */
+    public List<BibEntry> mindMap2Bibtex(MindMap mindMap) {
+        // Instantiate appropriate bib entries containing mind map, node, and edge data and return them all to be
+        // saved in the database
+        return null;
+    }
+
+    /**
+     * Helper method that takes a bib entry and iteratively converts the fields & values to those of a MindMapNode
+     */
+    private MindMapNode createNodeFromBibEntry(BibEntry entry) throws IllegalArgumentException {
+        // TODO: there's definitely a cleaner way to do this
+        MindMapNode newNode = new MindMapNode();
+        for (Map.Entry<Field, String> field : entry.getFieldMap().entrySet()) {
+            Field fieldName = field.getKey();
+            String fieldValue = field.getValue();
+            switch (fieldName.getName()) {
+                case MAP_NODE_ID -> newNode.setId(Long.parseLong(fieldValue));
+                case MAP_NODE_NAME -> newNode.setName(fieldValue);
+                case MAP_NODE_BIBENTRY -> newNode.setBibEntry(fieldValue);
+                case MAP_NODE_XPOS -> newNode.setX_pos(Integer.parseInt(fieldValue));
+                case MAP_NODE_YPOS -> newNode.setY_pos(Integer.parseInt(fieldValue));
+            }
+        }
+        return newNode;
+    }
+
+    /**
+     * Helper method that takes a bib entry and iteratively converts the fields & values to those of a MindMapEdge
+     */
+    private MindMapEdge createEdgeFromBibEntry(BibEntry entry) throws IllegalArgumentException {
+        MindMapEdge newEdge = new MindMapEdge();
+        for (Map.Entry<Field, String> field : entry.getFieldMap().entrySet()) {
+            Field fieldName = field.getKey();
+            String fieldValue = field.getValue();
+            switch (fieldName.getName()) {
+                case MAP_EDGE_NODE1_ID -> newEdge.setNode1_Id(Long.parseLong(fieldValue));
+                case MAP_EDGE_NODE2_ID -> newEdge.setNode2_Id(Long.parseLong(fieldValue));
+                case MAP_EDGE_LABEL -> newEdge.setLabel(fieldValue);
+                case MAP_EDGE_DIRECTION -> newEdge.setDirection(EdgeDirection.valueOf(fieldValue));
+            }
+        }
+        return newEdge;
+    }
+}