Inside of your {CATALINA_HOME}/conf/ folder exists a server.xml and context.xml file. Each one of these contains similar code, but references different parts of Tomcat to complete the same task.

server.xml is server-wide configuration. This is where you can set up HTTPS, HTTP2, JNDI Resources, etc.

context.xml is specific to each context in Tomcat, taken from Tomcat's documentation it explains this well:

The Context element represents a web application, which is run within a particular virtual host. Each web application is based on a Web Application Archive (WAR) file, or a corresponding directory containing the corresponding unpacked contents, as described in the Servlet Specification (version 2.2 or later). For more information about web application archives, you can download the Servlet Specification, and review the Tomcat Application Developer's Guide.

Essentially, it's application-specific configuration.

In order to operate correctly, we'll need to set up a Resource in server.xml and a reference to that resource inside of context.xml.

Inside of server.xml's <GlobalNamingResources> element, we'll append a new <Resource> which will be our JNDI reference:

 <GlobalNamingResources> 
    <!-- 
      JNDI Connection Pool for AS400
      Since it uses an older version of JDBC, we have to specify a validationQuery 
      to bypass errornous calls to isValid() (which doesn't exist in older JDBC)
    -->
    <Resource name="jdbc/SomeDataSource"
              auth="Container"
              type="javax.sql.DataSource"
              maxTotal="100"
              maxIdle="30"
              maxWaitMillis="10000"
              username="[databaseusername]"
              password="[databasepassword]"
              driverClassName="com.ibm.as400.access.AS400JDBCDriver"
              validationQuery="Select 1 from LIBRARY.TABLE"
              url="jdbc:as400://[yourserver]:[port]"/>

In this example, we're using a rather particular datasource (an IBMi - running DB2), which requires a validationQuery element set since it's using an older version of JDBC. This example is given as there is very little examples out there, as well as a display of the interoperability that a JDBC system affords you, even for an antiquated DB2 system (as above). Similar configuration would be the same for other popular database systems:

<Resource name="jdbc/SomeDataSource"
    auth="Container"
    type="javax.sql.DataSource"
    username="[DatabaseUsername]"
    password="[DatabasePassword]"
    driverClassName="com.mysql.jdbc.Driver"
    url="jdbc:mysql:/[yourserver]:[port]/[yourapplication]"
    maxActive="15"
    maxIdle="3"/>

Inside of context.xml we'll need to configure a "pointer" towards our jdbc datasource (which we made with a JNDI reference):

<Context>
    ...
    <ResourceLink name="jdbc/SomeDataSource"
      global="jdbc/SomeDataSource"
      type="javax.sql.DataSource" />
</Context>

Utilizing ResourceLink inside of context.xml allows us to reference the same datasource across applications and have it configured at the server level for multiple-database systems. (Although it also works just as well with one database)

public void test() {
    Connection conn = null;
    Statement stmt = null;
    try {
        Context ctx = (Context) new InitialContext().lookup("java:comp/env");
        conn = ((DataSource) ctx.lookup("jdbc/SomeDataSource")).getConnection();

        stmt = conn.createStatement();
        //SQL data fetch using the connection
        ResultSet rs = stmt.executeQuery("SELECT * FROM TABLE");
        while (rs.next()) {
            System.out.println(rs.getString("Id"));
        }
        conn.close();
        conn = null;
    }
    catch(Exception e){
        e.printStackTrace();
    }
    finally {

        if (stmt != null || conn != null) try {
            assert stmt != null;
            stmt.close();
        } catch (SQLException ex) {
            // ignore -- as we can't do anything about it here
            ex.printStackTrace();
        }
    }
}