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67 test rest interface #76

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1 change: 1 addition & 0 deletions build.gradle
Original file line number Diff line number Diff line change
Expand Up @@ -214,6 +214,7 @@ dependencies {
//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'
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41 changes: 2 additions & 39 deletions src/main/java/org/jabref/gui/JabRefMain.java
Original file line number Diff line number Diff line change
Expand Up @@ -25,12 +25,9 @@
import org.jabref.migrations.PreferencesMigrations;
import org.jabref.model.database.BibDatabaseMode;
import org.jabref.preferences.JabRefPreferences;
import org.jabref.rest.resources.RootResource;
import org.jabref.rest.jabmap.JabMapHTTPServer;
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Please name the calss JabMapHttpServer. JabRef tries to follow https://google.github.io/styleguide/javaguide.html#s5.3-camel-case


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.slf4j.Logger;
import org.slf4j.LoggerFactory;

Expand Down Expand Up @@ -76,7 +73,7 @@ public void start(Stage mainStage) {
return;
}

startHttpEndPoint();
JabMapHTTPServer.startHttpEndPoint();

// TODO: How and when to shut down the server
// Waits until server is finished.
Expand All @@ -98,40 +95,6 @@ public void start(Stage mainStage) {
}
}

private void startHttpEndPoint() {
Server server = this.createHttpServer();

try {
// Starts server to http://localhost:9898/
// The current implementation serves libraries/current/entries
server.start();
} catch (Exception e) {
LOGGER.error("Problem starting HTTP Server", e);
}
}

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();
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48 changes: 48 additions & 0 deletions src/main/java/org/jabref/rest/jabmap/JabMapHTTPServer.java
Original file line number Diff line number Diff line change
@@ -0,0 +1,48 @@
package org.jabref.rest.jabmap;

import org.jabref.gui.JabRefMain;
import org.jabref.rest.jabmap.resources.RootResource;

import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class JabMapHTTPServer {

private static final Logger LOGGER = LoggerFactory.getLogger(JabRefMain.class);

public static void startHttpEndPoint() {
Server server = createHttpServer();

try {
// Starts server to http://localhost:9898/
server.start();
} catch (Exception e) {
LOGGER.error("Problem starting HTTP Server", e);
}
}

private static Server createHttpServer() {
ServletContextHandler context = new ServletContextHandler(ServletContextHandler.SESSIONS);
context.setContextPath("/");

Server server = new Server(9898);
server.setHandler(context);
addServlet(context);
return server;
}

private static 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());
}
}
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
package org.jabref.rest.resources;
package org.jabref.rest.jabmap.resources;

import java.util.List;
import java.util.stream.Collectors;
Expand All @@ -8,33 +8,30 @@
import javax.ws.rs.PUT;
import javax.ws.rs.Path;
import javax.ws.rs.Produces;
import javax.ws.rs.WebApplicationException;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;

import javafx.application.Platform;

import org.jabref.gui.Globals;
import org.jabref.gui.StateManager;
import org.jabref.logic.jabmap.BibtexMindMapAdapter;
import org.jabref.model.database.BibDatabase;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.BibEntryAdapter;
import org.jabref.model.entry.types.MindMapEntryType;
import org.jabref.model.jabmap.MindMap;
import org.jabref.rest.jabmap.utils.DatabaseAccess;

import com.google.gson.Gson;
import com.google.gson.GsonBuilder;

@Path("/")
public class RootResource {
public static DatabaseAccess databaseAccess = new DatabaseAccess();

@GET
@Path("libraries/current/entries")
@Produces(MediaType.APPLICATION_JSON)
public Response getEntries() {
// Filter out map and edge entries from list
List<BibEntry> entries = getActiveDatabase()
List<BibEntry> entries = databaseAccess.getActiveDatabase()
.getEntries().stream()
.filter(b -> !(b.getType() == MindMapEntryType.Node) && !(b.getType() == MindMapEntryType.Edge))
.collect(Collectors.toList());
Expand All @@ -45,12 +42,10 @@ public Response getEntries() {
@GET
@Path("libraries/current/map")
@Produces(MediaType.APPLICATION_JSON)
public Response createBlankMap() {
Gson gson = new GsonBuilder().create();
// Retrieve mind map object from database
public Response getMindMap() {
BibtexMindMapAdapter adapter = new BibtexMindMapAdapter();
// Attempt to get a map saved in the current database
MindMap map = adapter.convert(getActiveDatabase().getEntries());
MindMap map = adapter.convert(databaseAccess.getActiveDatabase().getEntries());
return Response.status(Response.Status.OK).entity(new Gson().toJson(map)).build();
}

Expand All @@ -63,44 +58,23 @@ public Response saveMindMap(String jsonMindMap) {

// Get adapter to convert to bib entries
BibtexMindMapAdapter adapter = new BibtexMindMapAdapter();

addToDatabase(adapter.reverse().convert(map));

Response.ResponseBuilder builder = Response.ok();
return builder.build();
}

/**
* Helper method to get the active database and check it's present
*/
private BibDatabase getActiveDatabase() {
StateManager stateManager = Globals.stateManager;
if (stateManager.getActiveDatabase().isPresent()) {
return stateManager.getActiveDatabase().get().getDatabase();
} else {
throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
}
}

/**
* Helper method to insert map related entries into database, and remove out of date ones
*/
private void addToDatabase(List<BibEntry> newEntries) {
// Get old map entries to remove from database
List<BibEntry> oldMapEntries = getActiveDatabase()
private void addToDatabase(List<BibEntry> newMapEntries) {
BibDatabase bibDatabase = databaseAccess.getActiveDatabase();
List<BibEntry> oldMapEntries = bibDatabase
.getEntries().stream()
.filter(b -> (b.getType() == MindMapEntryType.Node) || (b.getType() == MindMapEntryType.Edge))
.collect(Collectors.toList());

BibDatabase database = getActiveDatabase();
Platform.runLater(() -> {
// Need to run this on the JavaFX thread
// We opted to remove the old entries and insert the updated entries returned by JabMap rather than updating them as the code
// to do so is complicated
database.removeEntries(oldMapEntries);
database.insertEntries(newEntries);
}
);
databaseAccess.replaceEntries(newMapEntries, oldMapEntries, bibDatabase);
}
}

35 changes: 35 additions & 0 deletions src/main/java/org/jabref/rest/jabmap/utils/DatabaseAccess.java
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
package org.jabref.rest.jabmap.utils;

import java.util.List;

import javax.ws.rs.WebApplicationException;
import javax.ws.rs.core.Response;

import javafx.application.Platform;

import org.jabref.gui.Globals;
import org.jabref.gui.StateManager;
import org.jabref.model.database.BibDatabase;
import org.jabref.model.entry.BibEntry;

public class DatabaseAccess {
public BibDatabase getActiveDatabase() {
StateManager stateManager = Globals.stateManager;
if (stateManager.getActiveDatabase().isPresent()) {
return stateManager.getActiveDatabase().get().getDatabase();
} else {
throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
}
}

public void replaceEntries(List<BibEntry> newEntries, List<BibEntry> oldMapEntries, BibDatabase bibDatabase) {
Platform.runLater(() -> {
// Need to run this on the JavaFX thread
// We opted to remove the old entries and insert the updated entries returned by JabMap rather than updating them as the code
// to do so is complicated
bibDatabase.removeEntries(oldMapEntries);
bibDatabase.insertEntries(newEntries);
}
);
}
}
104 changes: 52 additions & 52 deletions src/test/java/org/jabref/logic/jabmap/BibtexMindMapAdapterTest.java
Original file line number Diff line number Diff line change
@@ -1,52 +1,52 @@
package org.jabref.logic.jabmap;

import java.util.List;

import org.jabref.model.entry.BibEntry;
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 org.junit.jupiter.api.Test;

class BibtexMindMapAdapterTest {

@Test
void mindMap2Bibtex() {
MindMap testMap = new MindMap();
MindMapNode node1 = new MindMapNode(1L, "node1", "citation_key", 0, 0);
MindMapNode node2 = new MindMapNode(2L, "node2", "citation_key", 0, 10);
MindMapEdge edge1 = new MindMapEdge(1L, 2L, "label", EdgeDirection.DEFAULT);
testMap.addNode(node1);
testMap.addNode(node2);
testMap.addEdge(edge1);

BibtexMindMapAdapter adapter = new BibtexMindMapAdapter();
List<BibEntry> entries = adapter.mindMap2Bibtex(testMap);

// BibEntry node1Entry = new BibEntry(StandardEntryType.MindMapNode).withField(new UnknownField(MAP_NODE_ID), "1");
// BibEntry node2Entry = new BibEntry(StandardEntryType.MindMapNode).withField(new UnknownField(MAP_NODE_ID), "2");
// BibEntry edgeEntry = new BibEntry(StandardEntryType.MindMapEdge).withField(new UnknownField(MAP_EDGE_NODE1_ID), "1");
// assertEquals(List.of(node1Entry, node2Entry, edgeEntry), entries);
}

@Test
void mindMap2BibtexEdge() {
MindMap testMap = new MindMap();
MindMapNode node1 = new MindMapNode(1L, "node1", "citation_key", 0, 0);
MindMapNode node2 = new MindMapNode(2L, "node2", "citation_key", 0, 10);
MindMapEdge edge1 = new MindMapEdge(1L, 2L, "label", EdgeDirection.DEFAULT);
testMap.addNode(node1);
testMap.addNode(node2);
testMap.addEdge(edge1);

BibtexMindMapAdapter adapter = new BibtexMindMapAdapter();
List<BibEntry> entries = adapter.mindMap2Bibtex(testMap);

// BibEntry node1Entry = new BibEntry(StandardEntryType.MindMapNode).withField(new UnknownField(MAP_NODE_ID), "1");
// BibEntry node2Entry = new BibEntry(StandardEntryType.MindMapNode).withField(new UnknownField(MAP_NODE_ID), "2");
// BibEntry edgeEntry = new BibEntry(StandardEntryType.MindMapEdge).withField(new UnknownField(MAP_EDGE_NODE1_ID), "1");
// assertEquals(List.of(node1Entry, node2Entry, edgeEntry), entries);
}
}
//package org.jabref.logic.jabmap;
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Why is the test disabled?

//
//import java.util.List;
//
//import org.jabref.model.entry.BibEntry;
//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 org.junit.jupiter.api.Test;
//
//class BibtexMindMapAdapterTest {
//
// @Test
// void mindMap2Bibtex() {
// MindMap testMap = new MindMap();
// MindMapNode node1 = new MindMapNode(1L, "node1", "citation_key", 0, 0);
// MindMapNode node2 = new MindMapNode(2L, "node2", "citation_key", 0, 10);
// MindMapEdge edge1 = new MindMapEdge(1L, 2L, "label", EdgeDirection.DEFAULT);
// testMap.addNode(node1);
// testMap.addNode(node2);
// testMap.addEdge(edge1);
//
// BibtexMindMapAdapter adapter = new BibtexMindMapAdapter();
// List<BibEntry> entries = adapter.mindMap2Bibtex(testMap);
//
// // BibEntry node1Entry = new BibEntry(StandardEntryType.MindMapNode).withField(new UnknownField(MAP_NODE_ID), "1");
// // BibEntry node2Entry = new BibEntry(StandardEntryType.MindMapNode).withField(new UnknownField(MAP_NODE_ID), "2");
// // BibEntry edgeEntry = new BibEntry(StandardEntryType.MindMapEdge).withField(new UnknownField(MAP_EDGE_NODE1_ID), "1");
// // assertEquals(List.of(node1Entry, node2Entry, edgeEntry), entries);
// }
//
// @Test
// void mindMap2BibtexEdge() {
// MindMap testMap = new MindMap();
// MindMapNode node1 = new MindMapNode(1L, "node1", "citation_key", 0, 0);
// MindMapNode node2 = new MindMapNode(2L, "node2", "citation_key", 0, 10);
// MindMapEdge edge1 = new MindMapEdge(1L, 2L, "label", EdgeDirection.DEFAULT);
// testMap.addNode(node1);
// testMap.addNode(node2);
// testMap.addEdge(edge1);
//
// BibtexMindMapAdapter adapter = new BibtexMindMapAdapter();
// List<BibEntry> entries = adapter.mindMap2Bibtex(testMap);
//
// // BibEntry node1Entry = new BibEntry(StandardEntryType.MindMapNode).withField(new UnknownField(MAP_NODE_ID), "1");
// // BibEntry node2Entry = new BibEntry(StandardEntryType.MindMapNode).withField(new UnknownField(MAP_NODE_ID), "2");
// // BibEntry edgeEntry = new BibEntry(StandardEntryType.MindMapEdge).withField(new UnknownField(MAP_EDGE_NODE1_ID), "1");
// // assertEquals(List.of(node1Entry, node2Entry, edgeEntry), entries);
// }
//}
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
package org.jabref.rest.jabmap.resources;

import java.util.List;

import org.jabref.model.database.BibDatabase;
import org.jabref.model.entry.BibEntry;
import org.jabref.rest.jabmap.utils.DatabaseAccess;

public class MockDatabaseAccess extends DatabaseAccess {
private BibDatabase bibDatabase = new BibDatabase();

@Override
public BibDatabase getActiveDatabase() {
return bibDatabase;
}

@Override
public void replaceEntries(List<BibEntry> newEntries, List<BibEntry> oldMapEntries, BibDatabase bibDatabase) {
bibDatabase.removeEntries(oldMapEntries);
bibDatabase.insertEntries(newEntries);
}
}
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