是否可以将Gephi-0.8.2与Neo4j-2.1.8一起使用？

Question

我读到的关于Gephi-0.8.2的内容是我应该使用Neo4j-2.1.3，但我也注意到服务器不再可供下载。

将Gephi-0.8.2与Neo4j-2.1.8一起使用，我试图加载数据库图。我使用Import Traversal选项执行此操作，并在Gephi的日志文件中捕获以下异常，

WARNING [org.openide.filesystems.Ordering]: Found same position 600 for    
both Menu/File/org-gephi-desktop-importer-ImportDB.instance and 
Menu/File/org-gephi-desktop-neo4j-Neo4jMenuAction.instance
WARNING     [org.netbeans.modules.autoupdate.updateproviders.AutoupdateCatalogFactory]:  
  Services/AutoupdateType/org_gephi_branding_update_center.instance:  
  url_key attribute deprecated in favor of url
WARNING [org.netbeans.modules.autoupdate.updateproviders.AutoupdateCatalogFactory]:  
Services/AutoupdateType/org_gephi_branding_update_center_1.instance:  
url_key attribute deprecated in favor of url
WARNING [org.netbeans.TopSecurityManager]: use of system property 
netbeans.user has been obsoleted in favor of InstalledFileLocator/Places
at org.neo4j.kernel.info.SystemDiagnostics$7.dump 
(SystemDiagnostics.java:239)
SEVERE [global]
org.neo4j.graphdb.NotInTransactionException
at org.neo4j.kernel.impl.persistence.PersistenceManager.getCurrentTransaction(PersistenceManager.java:297)
at org.neo4j.kernel.impl.core.ThreadToStatementContextBridge.assertInTransaction(ThreadToStatementContextBridge.java:67)
at org.neo4j.tooling.GlobalGraphOperations.assertInTransaction(GlobalGraphOperations.java:236)
at org.neo4j.tooling.GlobalGraphOperations.getAllRelationshipTypes(GlobalGraphOperations.java:123)
at org.neo4j.kernel.InternalAbstractGraphDatabase.getRelationshipTypes(InternalAbstractGraphDatabase.java:1074)
at org.gephi.desktop.neo4j.ui.util.Neo4jUtils.relationshipTypeNames(Neo4jUtils.java:59)
at org.gephi.desktop.neo4j.ui.TraversalImportPanel.initComponents(TraversalImportPanel.java:191)
at org.gephi.desktop.neo4j.ui.TraversalImportPanel.<init>(TraversalImportPanel.java:55)
at org.gephi.desktop.neo4j.Neo4jMenuAction$TraversalImportMenuAction.showTraversalDialog(Neo4jMenuAction.java:379)
at org.gephi.desktop.neo4j.Neo4jMenuAction$TraversalImportMenuAction.actionPerformed(Neo4jMenuAction.java:334)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.AbstractButton.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$300(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown  
    Source)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown  
    Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
    [catch] at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:158)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

在此环境中是否存在任何正常工作方式？我的系统是Windows 8.1专业版。

一切顺利，

非常感谢。

Answer 1

最后我决定使用Gephi 0.9。问题是这个版本的应用程序没有配备Neo​​4j服务器的驱动程序，所以我不得不创建它并为这个新驱动程序调整应用程序。

以下是我所做的更改，

1）模块DBDrivers .-

我为Neo4j服务器创建了如下驱动程序，

public EdgeListPanel() {
    databaseManager = new EdgeListDatabaseManager();
    initComponents();

    driverComboBox.addItemListener(new ItemListener() {

        @Override
        public void itemStateChanged(ItemEvent ie) {
            initDriverType((SQLDriver) ie.getItem());
        }
    });

    browseButton.setVisible(false);
    browseButton.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent ae) {
            String lastPath = NbPreferences.forModule(EdgeListPanel.class).get(LAST_PATH, "");
            final JFileChooser chooser = new JFileChooser(lastPath);
            chooser.setAcceptAllFileFilterUsed(false);
            chooser.setDialogTitle(NbBundle.getMessage(EdgeListPanel.class, "EdgeListPanel.sqliteFileChooser.title"));
            DialogFileFilter dialogFileFilter = new DialogFileFilter(NbBundle.getMessage(EdgeListPanel.class, "EdgeListPanel.sqliteFileChooser.filefilter"));
            dialogFileFilter.addExtension("sqlite");

            dialogFileFilter.addExtension("neo4j"); //add extensión for neo4j

            dialogFileFilter.addExtension("db");
            chooser.addChoosableFileFilter(dialogFileFilter);

            int returnFile = chooser.showSaveDialog(null);
            if (returnFile != JFileChooser.APPROVE_OPTION) {
                return;
            }
            File file = chooser.getSelectedFile();
            hostTextField.setText(file.getAbsolutePath());

            //Save last path
            NbPreferences.forModule(EdgeListPanel.class).put(LAST_PATH, file.getParentFile().getAbsolutePath());
        }
    });
}

2）模块ImportPluginUI .-

我在EdgeListPanel.java类文件的代码中做了一些更改，如下所示，

在构造函数中，我为Neo4j添加了extensión，

private void initDriverType(final SQLDriver driver) {
    SwingUtilities.invokeLater(new Runnable() {

        @Override
        public void run() {
            if (driver != null && driver.getPrefix().equals("sqlite")) {
                hostLabel.setText(NbBundle.getMessage(EdgeListPanel.class, "EdgeListPanel.fileLabel.text"));
                portTextField.setEnabled(false);
                portLabel.setEnabled(false);
                dbLabel.setEnabled(false);
                dbTextField.setEnabled(false);
                userLabel.setEnabled(false);
                userTextField.setEnabled(false);
                pwdLabel.setEnabled(false);
                pwdTextField.setEnabled(false);
                pwdTextField.setText("");
                userTextField.setText("");
                dbTextField.setText("");
                portTextField.setText("");
                browseButton.setVisible(true);


            } else if (driver != null && driver.getPrefix().equals("neo4j")) {
                hostLabel.setText(NbBundle.getMessage(EdgeListPanel.class, "EdgeListPanel.hostLabel.text"));
                portTextField.setEnabled(true);
                portLabel.setEnabled(true);
                dbLabel.setEnabled(false);
                dbTextField.setEnabled(false);
                userLabel.setEnabled(false);
                userTextField.setEnabled(false);
                pwdLabel.setEnabled(false);
                pwdTextField.setEnabled(false);
                pwdTextField.setText("");
                userTextField.setText("");
                dbTextField.setText("");
                browseButton.setVisible(false);


            } else {
                hostLabel.setText(NbBundle.getMessage(EdgeListPanel.class, "EdgeListPanel.hostLabel.text"));
                portTextField.setEnabled(true);
                portLabel.setEnabled(true);
                dbLabel.setEnabled(true);
                dbTextField.setEnabled(true);
                userLabel.setEnabled(true);
                userTextField.setEnabled(true);
                pwdLabel.setEnabled(true);
                pwdTextField.setEnabled(true);
                browseButton.setVisible(false);
            }
            group.validateAll();
        }
    });
}

在initDriverType（）方法中，我启用了Neo4j的面板，

private static boolean isValidDriverPrefix(EdgeListPanel panel, String prefix) {
    if (panel.databaseManager.getEdgeListDatabases().size() > 0) {
        if (panel.databaseManager.getEdgeListDatabases().get(0).getSQLDriver().getPrefix().equals(prefix)) {
            return true;
        }
        return false;
    } else if (panel.getSelectedSQLDriver().getPrefix().equals(prefix)) {
        return true;
    }
    return false;
}

以下方法是一种更通用的方法，然后旧方法是SQLite（），因为它让我传递我需要的任何前缀。在这种情况下，它们应该是“sqlite”和“neo4j”

private static class HostOrFileValidator implements Validator<String> {

    private EdgeListPanel panel;

    public HostOrFileValidator(EdgeListPanel panel) {
        this.panel = panel;
    }

    @Override
    public boolean validate(Problems problems, String compName, String model) {
        if (isValidDriverPrefix(panel, "sqlite")) {
            return Validators.FILE_MUST_BE_FILE.validate(problems, compName, model);
        } else {
            return Validators.REQUIRE_NON_EMPTY_STRING.validate(problems, compName, model);
        }
    }
}

private static class NotEmptyValidator implements Validator<String> {

    private EdgeListPanel panel;

    public NotEmptyValidator(EdgeListPanel panel) {
        this.panel = panel;
    }

    @Override
    public boolean validate(Problems problems, String compName, String model) {
        if (isValidDriverPrefix(panel, "sqlite") || isValidDriverPrefix(panel, "neo4j")) {
            return true;
        } else {
            return Validators.REQUIRE_NON_EMPTY_STRING.validate(problems, compName, model);
        }
    }
}

private static class PortValidator implements Validator<String> {

    private EdgeListPanel panel;

    public PortValidator(EdgeListPanel panel) {
        this.panel = panel;
    }

    @Override
    public boolean validate(Problems problems, String compName, String model) {
        if (isValidDriverPrefix(panel, "sqlite")) {
            return true;
        } else {
            return Validators.REQUIRE_NON_EMPTY_STRING.validate(problems, compName, model)
                    && Validators.REQUIRE_VALID_INTEGER.validate(problems, compName, model)
                    && Validators.numberRange(1, 65535).validate(problems, compName, model);
        }
    }
}

我在下面的内部类中使用它，

private void getNodes(Connection connection) throws SQLException {

    //Factory
    ElementDraftFactory factory = container.factory();

    //Properties
    PropertiesAssociations properties = database.getPropertiesAssociations();

    Statement s = connection.createStatement();
    ResultSet rs = null;
    try {
        rs = s.executeQuery(database.getNodeQuery());
    } catch (SQLException ex) {
        report.logIssue(new Issue("Failed to execute Node query", Issue.Level.SEVERE, ex));
        return;
    }

    findNodeAttributesColumns(rs);
    ResultSetMetaData metaData = rs.getMetaData();
    int columnsCount = metaData.getColumnCount();
    int count = 0;
    while (rs.next()) {
        String id = null;
        for (int i = 0; i < columnsCount; i++) {
            String columnName = metaData.getColumnLabel(i + 1);
            NodeProperties p = properties.getNodeProperty(columnName);

            if (p != null) { //Here p could be null

                if (p.equals(NodeProperties.ID)) {
                    String ide = rs.getString(i + 1);
                    if (ide != null) {
                        id = ide;
                    }
                }
            }
        }
        NodeDraft node;
        if (id != null) {
            node = factory.newNodeDraft(id);
        } else {
            node = factory.newNodeDraft();
        }

        for (int i = 0; i < columnsCount; i++) {
            String columnName = metaData.getColumnLabel(i + 1);
            NodeProperties p = properties.getNodeProperty(columnName);
            if (p != null) {
                injectNodeProperty(p, rs, i + 1, node);
            } else {
                //Inject node attributes
                ColumnDraft col = container.getNodeColumn(columnName);
                injectElementAttribute(rs, i + 1, col, node);
            }
        }
        // injectTimeIntervalProperty(node);
        container.addNode(node);
        ++count;
    }
    rs.close();
    s.close();

}

private void getEdges(Connection connection) throws SQLException {

    //Factory
    ElementDraftFactory factory = container.factory();

    //Properties
    PropertiesAssociations properties = database.getPropertiesAssociations();

    Statement s = connection.createStatement();
    ResultSet rs = null;
    try {
        rs = s.executeQuery(database.getEdgeQuery());
    } catch (SQLException ex) {
        report.logIssue(new Issue("Failed to execute Edge query", Issue.Level.SEVERE, ex));
        return;
    }
    findEdgeAttributesColumns(rs);
    ResultSetMetaData metaData = rs.getMetaData();
    int columnsCount = metaData.getColumnCount();
    int count = 0;
    while (rs.next()) {
        String id = null;
        for (int i = 0; i < columnsCount; i++) {
            String columnName = metaData.getColumnLabel(i + 1);
            EdgeProperties p = properties.getEdgeProperty(columnName);

            if (p != null) { //Here p could be null

                if (p.equals(EdgeProperties.ID)) {
                    String ide = rs.getString(i + 1);
                    if (ide != null) {
                        id = ide;
                    }
                }
            }
        }
        EdgeDraft edge;
        if (id != null) {
            edge = factory.newEdgeDraft(id);
        } else {
            edge = factory.newEdgeDraft();
        }
        for (int i = 0; i < columnsCount; i++) {
            String columnName = metaData.getColumnLabel(i + 1);
            EdgeProperties p = properties.getEdgeProperty(columnName);
            if (p != null) {
                injectEdgeProperty(p, rs, i + 1, edge);
            } else {
                //Inject edge attributes
                ColumnDraft col = container.getEdgeColumn(columnName);
                injectElementAttribute(rs, i + 1, col, edge);
            }
        }
        // injectTimeIntervalProperty(edge);
        container.addEdge(edge);
        ++count;
    }
    rs.close();
    s.close();
}

3）模块ImportPlugin .-

在这个模块中，我必须调整类文件ImporterEdgeList.java，改变方法getNodes（）和getEdges（），因为它们在实现Neo4j图形数据库时抛出了NullPointerException。这很简单，

           ops =  {"+": operator.add,
                   "-": operator.sub,
                   "*": operator.mul,
                   "/": operator.div}

就是这样。

这些更改后的Gephi 0.9针对Neo4j 2.1.8电影数据库和Neo4j 2.3.0-M01的相同示例数据库进行了测试，但未进行身份验证。

希望它有所帮助！

Answer 2

要构建Gephi-0.9，最好使用最新的NetBeans IDE，并从https://github.com/gephi/gephi下载应用程序和源代码。

打开源代码，这是一个进入NetBeans IDE的maven项目，如果您愿意，可以提取相应的模块以将更改作为独立的maven项目进行。

完成后，将... \ target \ nbm \ netbeans \ gephi文件夹的内容复制到Gephi-0.9应用程序的相应... \ gephi \ gephi文件夹中，然后就可以了。

这是DBDrivers模块的pom.xml文件，

<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
    <artifactId>gephi-parent</artifactId>
    <groupId>org.gephi</groupId>
    <version>0.9-SNAPSHOT</version>
    <relativePath>../..</relativePath>
</parent>

<groupId>org.gephi</groupId>
<artifactId>db-drivers</artifactId>
<version>0.9-SNAPSHOT</version>
<packaging>nbm</packaging>

<name>DBDrivers</name>

<dependencies>
    <dependency>
        <groupId>org.xerial</groupId>
        <artifactId>sqlite-jdbc</artifactId>
        <version>3.7.2</version>
    </dependency>
    <dependency>
        <groupId>mysql</groupId>
        <artifactId>mysql-connector-java</artifactId>
        <version>5.1.18</version>
    </dependency>
    <dependency>
        <groupId>postgresql</groupId>
        <artifactId>postgresql</artifactId>
        <version>9.1-901-1.jdbc4</version>
    </dependency>
    <dependency>
        <groupId>com.microsoft.sqlserver</groupId>
        <artifactId>sqljdbc4</artifactId>
        <version>3.0.1301.101</version>
    </dependency>
    <dependency>
        <groupId>com.teradata</groupId>
        <artifactId>teradata-jdbc</artifactId>
        <version>14.00.00.21</version>
    </dependency>
    <dependency>
        <groupId>com.teradata</groupId>
        <artifactId>teradata-config</artifactId>
        <version>14.00.00.21</version>
    </dependency>
    <dependency>
        <groupId>org.neo4j</groupId>
        <artifactId>neo4j-jdbc</artifactId>
        <version>2.1.4</version>
    </dependency>
    <dependency>
        <groupId>org.netbeans.api</groupId>
        <artifactId>org-openide-util-lookup</artifactId>
    </dependency>
</dependencies>

<build>
    <plugins>
        <plugin>
            <groupId>org.codehaus.mojo</groupId>
            <artifactId>nbm-maven-plugin</artifactId>
            <configuration>
                <publicPackages>
                     <publicPackage>org.gephi.io.database.drivers</publicPackage>
                </publicPackages>
            </configuration>
        </plugin>
        <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-compiler-plugin</artifactId>
            <version>2.3.2</version>
            <configuration>
                <source>1.7</source>
                <target>1.7</target>
            </configuration>
        </plugin>
    </plugins>
  </build>
</project>