Update dependencies

src/pom.xml

@@ -89,7 +89,7 @@
         <dependency>
             <groupId>de.unibi.agbi.biodwh2</groupId>
             <artifactId>biodwh2-core</artifactId>
-            <version>0.4.6</version>
+            <version>0.4.13</version>
         </dependency>
         <dependency>
             <groupId>de.unibi.agbi.biodwh2</groupId>
@@ -99,27 +99,32 @@
         <dependency>
             <groupId>io.javalin</groupId>
             <artifactId>javalin</artifactId>
-            <version>4.6.4</version>
+            <version>5.6.3</version>
         </dependency>
         <dependency>
             <groupId>info.picocli</groupId>
             <artifactId>picocli</artifactId>
-            <version>4.6.3</version>
+            <version>4.7.5</version>
         </dependency>
         <dependency>
             <groupId>commons-codec</groupId>
             <artifactId>commons-codec</artifactId>
-            <version>1.15</version>
+            <version>1.16.0</version>
         </dependency>
         <dependency>
             <groupId>com.graphql-java</groupId>
             <artifactId>graphql-java</artifactId>
-            <version>19.2</version>
+            <version>21.3</version>
         </dependency>
         <dependency>
             <groupId>com.graphql-java</groupId>
             <artifactId>graphql-java-extended-scalars</artifactId>
-            <version>19.0</version>
+            <version>21.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-slf4j2-impl</artifactId>
+            <version>2.21.1</version>
         </dependency>
     </dependencies>
 

src/src/main/java/de/unibi/agbi/biodwh2/graphql/server/GraphQLServer.java

@@ -17,11 +17,12 @@
 import graphql.schema.idl.SchemaParser;
 import graphql.schema.idl.TypeDefinitionRegistry;
 import io.javalin.Javalin;
-import io.javalin.core.JavalinConfig;
+import io.javalin.config.JavalinConfig;
 import io.javalin.http.Context;
+import io.javalin.plugin.bundled.CorsPluginConfig;
 import org.apache.commons.lang3.StringUtils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import picocli.CommandLine;
 
 import java.awt.*;
@@ -36,7 +37,7 @@
 import java.util.stream.Collectors;
 
 public class GraphQLServer {
-    private static final Logger LOGGER = LoggerFactory.getLogger(GraphQLServer.class);
+    private static final Logger LOGGER = LogManager.getLogger(GraphQLServer.class);
     private static final String DATABASE_FILE_NAME = "mapped." + Graph.EXTENSION;
     private static final String SCHEMA_FILE_NAME = "mapped." + GraphQLSchemaWriter.EXTENSION;
 
@@ -123,8 +124,8 @@ private static RuntimeWiring buildRuntimeWiring(final Graph graph) {
     }
 
     private void configureJavalin(final JavalinConfig config) {
-        config.defaultContentType = "application/json";
-        config.enableCorsForAllOrigins();
+        config.http.defaultContentType = "application/json";
+        config.plugins.enableCors(cors -> cors.add(CorsPluginConfig::anyHost));
         config.showJavalinBanner = false;
     }
 
@@ -155,7 +156,7 @@ private static void handleRootPost(final Context ctx) throws IOException {
     }
 
     private static boolean isLineEmptyOrComment(final String l) {
-        return l.length() == 0 || l.trim().startsWith("#");
+        return l.isEmpty() || l.trim().startsWith("#");
     }
 
     private void openBrowser(final int port) {

src/src/main/java/de/unibi/agbi/biodwh2/graphql/server/model/GraphViewIds.java

@@ -41,6 +41,16 @@ public void removeEdgeIds(final Collection<Long> ids) {
         edgeIds.removeAll(ids);
     }
 
+    @Override
+    public Iterable<Long> getNodeIds(final String label) {
+        return () -> new FilterIdsIterator(nodeIds, graph.getNodeIds(label).iterator());
+    }
+
+    @Override
+    public Iterable<Long> getEdgeIds(final String label) {
+        return () -> new FilterIdsIterator(edgeIds, graph.getEdgeIds(label).iterator());
+    }
+
     @Override
     public Iterable<Node> getNodes() {
         return filterNodesIterable(graph.getNodes());
@@ -229,6 +239,36 @@ public Iterable<Edge> findEdges(final Map<String, Comparable<?>> properties) {
         return filterEdgesIterable(graph.findEdges(properties));
     }
 
+    private class FilterIdsIterator implements Iterator<Long> {
+        private final Set<Long> ids;
+        private final Iterator<Long> parent;
+        private Long nextNodeId = null;
+
+        FilterIdsIterator(final Set<Long> ids, final Iterator<Long> parent) {
+            this.ids = ids;
+            this.parent = parent;
+        }
+
+        @Override
+        public boolean hasNext() {
+            nextNodeId = null;
+            while (parent.hasNext()) {
+                nextNodeId = parent.next();
+                if (ids.contains(nextNodeId)) {
+                    break;
+                } else {
+                    nextNodeId = null;
+                }
+            }
+            return nextNodeId != null;
+        }
+
+        @Override
+        public Long next() {
+            return nextNodeId;
+        }
+    }
+
     private class FilterNodesIterator implements Iterator<Node> {
         private final Iterator<Node> parent;
         private Node nextNode = null;

src/src/main/resources/log4j2.xml

@@ -0,0 +1,12 @@
+<Configuration status="warn" name="biodwh2">
+    <Appenders>
+        <Console name="console" target="SYSTEM_OUT">
+            <PatternLayout pattern="%d{yyyy-MM-dd HH:mm:ss} [%-5p] %c:%L - %m%n%throwable"/>
+        </Console>
+    </Appenders>
+    <Loggers>
+        <Root level="info">
+            <AppenderRef ref="console"/>
+        </Root>
+    </Loggers>
+</Configuration>