Merge branch 'driver-upgrade'

Conflicts:
	pom.xml

pom.xml

@@ -14,12 +14,12 @@
      	<maven.test.skip>true</maven.test.skip>
         <bundle.symbolicName>nl.corwur.cytoscape.neo4j</bundle.symbolicName>
         <bundle.namespace>nl.corwur.cytoscape.neo4j</bundle.namespace>
-        <cytoscape.version>3.8.0</cytoscape.version>
+        <cytoscape.version>3.9.0</cytoscape.version>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <org.osgi.core.version>6.0.0</org.osgi.core.version>
         <neo4j-java-driver.version>4.4.1</neo4j-java-driver.version>
         <junit.version>4.13.1</junit.version>
-        <log4j.version>2.17.1</log4j.version>
+        <pax-logging.version>1.5.3</pax-logging.version>
         <maven-compiler-plugin.version>3.7.0</maven-compiler-plugin.version>
         <maven-bundle-plugin.version>4.2.1</maven-bundle-plugin.version>
         <mockito-core.version>3.3.3</mockito-core.version>

src/main/java/nl/corwur/cytoscape/neo4j/internal/configuration/AppConfiguration.java

@@ -1,7 +1,8 @@
 package nl.corwur.cytoscape.neo4j.internal.configuration;
 
-import org.apache.log4j.Logger;
-
+import nl.corwur.cytoscape.neo4j.internal.neo4j.ConnectionParameter;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -16,9 +17,14 @@
  */
 public class AppConfiguration {
 
-    private static final Logger LOG = Logger.getLogger(AppConfiguration.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(AppConfiguration.class);
+
+    private static final int BOLT_PORT = 7687;
+    private static final Logger LOG = LoggerFactory.getLogger(AppConfiguration.class);
     private static final String TEMPLATEDIR = "templatedir";
+    private static final String NEO4J_PROTOCOL = "neo4j.protocol";
     private static final String NEO4J_HOST = "neo4j.host";
+    private static final String NEO4J_PORT = "neo4j.port";
     private static final String NEO4J_USERNAME = "neo4j.username";
     private static final String NEO4J_DATABASE = "neo4j.database";
     private Properties properties = new Properties();
@@ -31,6 +37,25 @@ public String getNeo4jHost() {
         return properties.getProperty(NEO4J_HOST);
     }
 
+    public ConnectionParameter.Protocol getNeo4jProtocol() {
+        try {
+            return ConnectionParameter.Protocol.valueOf(properties.getProperty(NEO4J_PROTOCOL));
+        } catch (IllegalArgumentException e) {
+            LOGGER.warn("Invalid protocol using bolt:// {}", e);
+            return ConnectionParameter.Protocol.BOLT;
+        }
+    }
+
+    public int getNeo4jPort() {
+        try {
+            return Integer.parseInt(properties.getProperty(NEO4J_PORT));
+        } catch (NumberFormatException e) {
+            LOGGER.warn("Invalid port number using default bolt port (7687) {}", e);
+            return BOLT_PORT;
+        }
+    }
+
+
     public String getNeo4jUsername() {
         return properties.getProperty(NEO4J_USERNAME);
     }
@@ -56,6 +81,8 @@ public void load() {
     }
 
     private void setDefaultProperties() {
+        properties.setProperty(NEO4J_PROTOCOL, "BOLT");
+        properties.setProperty(NEO4J_PORT, "7687");
         properties.setProperty(NEO4J_HOST, "localhost");
         properties.setProperty(NEO4J_USERNAME, "neo4j");
         properties.setProperty(NEO4J_DATABASE, "neo4j");
@@ -76,7 +103,8 @@ private Path getConfigurationFile() {
         return Paths.get(tmpDir, "corwur-cyneo4j.properties");
     }
 
-    public void setConnectionParameters(String hostname, String username, String database) {
+    public void setConnectionParameters(String protocol,String hostname, String username, String database) {
+        properties.setProperty(NEO4J_PROTOCOL, protocol);
         properties.setProperty(NEO4J_HOST, hostname);
         properties.setProperty(NEO4J_USERNAME, username);
         properties.setProperty(NEO4J_DATABASE, database);

src/main/java/nl/corwur/cytoscape/neo4j/internal/neo4j/ConnectionParameter.java

@@ -1,20 +1,41 @@
 package nl.corwur.cytoscape.neo4j.internal.neo4j;
 
 public class ConnectionParameter {
-    private final String host;
+
+    public enum Protocol {
+        BOLT("bolt"),
+        NEO4J("neo4j");
+
+
+        private final String protocol;
+        Protocol(String protocol) {
+            this.protocol = protocol;
+        }
+
+    }
+
+    private final int port;
+    private final Protocol protocol;
+    private final String hostname;
     private final String username;
     private final char[] password;
     private final String database;
 
-    public ConnectionParameter(String url, String username, char[] password, String database) {
-        this.host = url;
+    public ConnectionParameter(Protocol protocol, String hostname, int port, String username, char[] password, String database) {
+        this.protocol = protocol;
+        this.hostname = hostname;
         this.username = username;
         this.password = password;
         this.database = database;
+        this.port = port;
+    }
+
+    String getUrl() {
+        return protocol.protocol + "://" + hostname + ":" + port;
     }
 
-    String getBoltUrl() {
-        return "neo4j://" + host;
+    Protocol getProtocol() {
+        return protocol;
     }
 
     String getUsername() {

src/main/java/nl/corwur/cytoscape/neo4j/internal/neo4j/Neo4jClient.java

@@ -1,5 +1,7 @@
 package nl.corwur.cytoscape.neo4j.internal.neo4j;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import nl.corwur.cytoscape.neo4j.internal.graph.Graph;
 
 import java.util.List;
@@ -9,7 +11,7 @@
 import org.neo4j.driver.exceptions.ServiceUnavailableException;
 
 public class Neo4jClient {
-    private static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(Neo4jClient.class);
+    private static Logger logger = LoggerFactory.getLogger(Neo4jClient.class);
 
     private Driver driver;
     private Neo4jGraphFactory neo4JGraphFactory = new Neo4jGraphFactory();
@@ -18,7 +20,7 @@ public class Neo4jClient {
     public boolean connect(ConnectionParameter connectionParameter) {
         try {
             driver = GraphDatabase.driver(
-                    connectionParameter.getBoltUrl(),
+                    connectionParameter.getUrl(),
                     AuthTokens.basic(
                             connectionParameter.getUsername(),
                             connectionParameter.getPasswordAsString()
@@ -34,7 +36,11 @@ public boolean connect(ConnectionParameter connectionParameter) {
     }
 
     private Session getSession(){
-        return driver.session(SessionConfig.builder().withDatabase(database).build());
+        if(driver.supportsMultiDb()) {
+            return driver.session(SessionConfig.builder().withDatabase(database).build());
+        } else {
+            return driver.session(SessionConfig.builder().build());
+        }
     }
 
     public void executeQuery(CypherQuery cypherQuery) throws Neo4jClientException {

src/main/java/nl/corwur/cytoscape/neo4j/internal/tasks/querytemplate/mapping/values/ValueScriptExpression.java

@@ -1,7 +1,7 @@
 package nl.corwur.cytoscape.neo4j.internal.tasks.querytemplate.mapping.values;
 
-import org.apache.log4j.Logger;
-
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import javax.script.ScriptEngine;
 import javax.script.ScriptEngineManager;
 import javax.script.ScriptException;
@@ -14,7 +14,7 @@
  */
 public abstract class ValueScriptExpression<T, V> implements ValueExpression<T, V> {
 
-    private Logger logger = Logger.getLogger(ValueScriptExpression.class);
+    private Logger logger = LoggerFactory.getLogger(ValueScriptExpression.class);
 
     private final String script;
     private final String varName;
@@ -33,7 +33,7 @@ public V eval(T val) {
         try {
             return type.cast(engine.eval(script));
         } catch (ScriptException | ClassCastException e) {
-            logger.error(e);
+            logger.error("{}",e);
             return null;
         }
     }

src/main/java/nl/corwur/cytoscape/neo4j/internal/tasks/querytemplate/provider/CypherQueryTemplateDirectoryProvider.java

@@ -4,7 +4,8 @@
 import nl.corwur.cytoscape.neo4j.internal.tasks.querytemplate.template.Reader;
 import nl.corwur.cytoscape.neo4j.internal.tasks.querytemplate.template.ReaderException;
 import nl.corwur.cytoscape.neo4j.internal.tasks.querytemplate.template.Writer;
-import org.apache.log4j.Logger;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.xml.bind.JAXBException;
 import java.io.IOException;
@@ -21,7 +22,7 @@
 
 public class CypherQueryTemplateDirectoryProvider {
 
-    private static Logger logger = Logger.getLogger(CypherQueryTemplateDirectoryProvider.class);
+    private static Logger logger = LoggerFactory.getLogger(CypherQueryTemplateDirectoryProvider.class);
 
     private Map<Long, TemplateMapEntry> cypherQueryTemplateMap = new HashMap<>();
 

src/main/java/nl/corwur/cytoscape/neo4j/internal/ui/connect/ConnectDialog.java

@@ -11,18 +11,28 @@ class ConnectDialog extends JDialog { //NOSONAR , hierarchy level > 5
 
     private static final String CANCEL_CMD = "cancel";
     private static final String OK_CMD = "ok";
+
+    private JComboBox protocolCombobox = new JComboBox(ConnectionParameter.Protocol.values());
     private JTextField usernameField = new JTextField("neo4j");
     private JTextField hostnameField = new JTextField("localhost");
+    private JTextField portField = new JTextField("7687");
     private JTextField databaseField = new JTextField("database");
     private JPasswordField password = new JPasswordField();
     private boolean ok = false;
     private final transient Predicate<ConnectionParameter> connectionCheck;
 
-    ConnectDialog(JFrame jFrame, Predicate<ConnectionParameter> connectionCheck, String hostname, String username, String database) {
+    ConnectDialog(JFrame jFrame, Predicate<ConnectionParameter> connectionCheck,
+                  ConnectionParameter.Protocol protocol,
+                  int port,
+                  String hostname,
+                  String username,
+                  String database) {
         super(jFrame);
         this.connectionCheck = connectionCheck;
+        protocolCombobox.setSelectedItem(protocol);
         usernameField.setText(username);
         hostnameField.setText(hostname);
+        portField.setText(String.valueOf(port));
         databaseField.setText(database);
     }
 
@@ -33,7 +43,7 @@ void showConnectDialog() {
         setModal(true);
         setResizable(true);
         pack();
-        setSize(380, 240);
+        setSize(380, 280);
         setVisible(true);
     }
 
@@ -54,7 +64,13 @@ void setDatabaseField(String database){
     }
 
     private ConnectionParameter getParameters() {
-        return new ConnectionParameter(hostnameField.getText(), usernameField.getText(), password.getPassword(), databaseField.getText());
+        return new ConnectionParameter(
+                (ConnectionParameter.Protocol) protocolCombobox.getSelectedItem(),
+                hostnameField.getText(),
+                Integer.parseInt(portField.getText()),
+                usernameField.getText(),
+                password.getPassword(),
+                databaseField.getText());
     }
 
     private void init() {
@@ -72,7 +88,9 @@ private void init() {
         cancelButton.addActionListener(ae -> dispose());
         cancelButton.setActionCommand(CANCEL_CMD);
 
+        JLabel protocolLabel = new JLabel("Protocol");
         JLabel hostnameLabel = new JLabel("Hostname");
+        JLabel portLabel = new JLabel("Port");
         JLabel databaseLabel = new JLabel("Database");
         JLabel usernameLabel = new JLabel("Username");
         JLabel passwordLabel = new JLabel("Password");
@@ -84,53 +102,83 @@ private void init() {
         GridBagConstraints gbc = new GridBagConstraints();
         gbc.insets = new Insets(4, 4, 4, 4);
 
+        int y = 0;
+        //Protocol
+        gbc.gridx = 0;
+        gbc.gridy = y;
+        gbc.weightx = 0;
+        topPanel.add(protocolLabel, gbc);
+
+        gbc.gridx = 1;
+        gbc.gridy = y;
+        gbc.fill = GridBagConstraints.HORIZONTAL;
+        gbc.weightx = 1;
+        topPanel.add(protocolCombobox, gbc);
+
         //Hostname
+        y++;
         gbc.gridx = 0;
-        gbc.gridy = 0;
+        gbc.gridy = y;
         gbc.weightx = 0;
         topPanel.add(hostnameLabel, gbc);
 
         gbc.gridx = 1;
-        gbc.gridy = 0;
+        gbc.gridy = y;
         gbc.fill = GridBagConstraints.HORIZONTAL;
         gbc.weightx = 1;
         topPanel.add(hostnameField, gbc);
 
+        //Port
+        y++;
+        gbc.gridx = 0;
+        gbc.gridy = y;
+        gbc.weightx = 0;
+        topPanel.add(portLabel, gbc);
+
+        gbc.gridx = 1;
+        gbc.gridy = y;
+        gbc.fill = GridBagConstraints.HORIZONTAL;
+        gbc.weightx = 1;
+        topPanel.add(portField, gbc);
+
         //Database name
+        y++;
         gbc.gridx = 0;
-        gbc.gridy = 1;
+        gbc.gridy = y;
         gbc.fill = GridBagConstraints.NONE;
         gbc.weightx = 0;
         topPanel.add(databaseLabel, gbc);
 
         gbc.gridx = 1;
-        gbc.gridy = 1;
+        gbc.gridy = y;
         gbc.fill = GridBagConstraints.HORIZONTAL;
         gbc.weightx = 0;
         topPanel.add(databaseField, gbc);
 
         //Username
+        y++;
         gbc.gridx = 0;
-        gbc.gridy = 2;
+        gbc.gridy = y;
         gbc.fill = GridBagConstraints.NONE;
         gbc.weightx = 0;
         topPanel.add(usernameLabel, gbc);
 
         gbc.gridx = 1;
-        gbc.gridy = 2;
+        gbc.gridy = y;
         gbc.fill = GridBagConstraints.HORIZONTAL;
         gbc.weightx = 0;
         topPanel.add(usernameField, gbc);
 
         //Password
+        y++;
         gbc.gridx = 0;
-        gbc.gridy = 3;
+        gbc.gridy = y;
         gbc.fill = GridBagConstraints.NONE;
         gbc.weightx = 0;
         topPanel.add(passwordLabel, gbc);
 
         gbc.gridx = 1;
-        gbc.gridy = 3;
+        gbc.gridy = y;
         gbc.fill = GridBagConstraints.HORIZONTAL;
         gbc.weightx = 0;
         topPanel.add(password, gbc);
@@ -151,7 +199,9 @@ private void ok() {
     }
 
     public static void main(String[] args) {
-        ConnectDialog connectDialog = new ConnectDialog(null, connectionParameter -> true, "localhost", "neo4j", "neo4j");
+        ConnectDialog connectDialog = new ConnectDialog(null, connectionParameter -> true,
+                ConnectionParameter.Protocol.BOLT, 7687,
+                "localhost", "neo4j", "neo4j");
         connectDialog.showConnectDialog();
 
     }
@@ -167,4 +217,8 @@ public String getUsername() {
     public String getDatabase() {
         return databaseField.getText();
     }
+
+    public String getProtocol() {
+        return protocolCombobox.getSelectedItem().toString();
+    }
 }