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Use Jolokia to monitor JMX endpoint of webapp on same Tomcat server

Jolokia is uncharted territory for me, and after having read the documentation, I'm still not sure if it'll work with the scenario I have in mind.
Setup:
Tomcat application server (version ranges from 6.x to 7.x), usually on a Windows platform, occasionally a flavour of Linux.
Deployed third-party Java web application (SAP BusinessObjects) with JMX monitoring enabled (accessible through RMI).
Possible gotcha's:
The Java web application to be monitored is commercial and closed source, so modifications are not possible. The only thing that can be changed is the JMX port number
The JMX endpoint is a custom one, thus not the default jmxrmi endpoint.
The JMX connection requires authentication.
Goal:
What I'd like to do is to deploy the Jolokia WAR file onto the Tomcat server and then configure it so that I can read the MBean attributes from the other web application.
I would code the client myself using Python (version 3) and the Requests HTTP library.
I've been reading through the Jolokia documentation (again, I'm a complete newbie at this point), but can't figure out if this would be possible or not (as I can't seem to find where to enter the JMX/RMI url or the authentication information).
Questions:
Can I use the WAR agent for this setup?
If not, can you please explain why (so I can understand, not because I don't believe you). Also, is there another agent that's more suited for this scenario?
If yes, can you point me in the right direction how to configure the Jolokia to the web application to connect to?

First of all, Jolokia by passes the JSR-160 connector stuff completely, so there is no need for any JMX/RMI authentication. The whole purpose of Jolokia is to provide a bridge over HTTP/JSON to the internal JMX subsystem. Depending on the agent, you can secure Jolokia quite easily. For the WAR agent, securing is the same as for any Java EE web app: Setup some roles and users for tomcat (e.g. in tomcat-users.xml) and reference the role in the security contstraints within the jolokia.war's /WEB-INF/web.xml.
To your questions:
Yes, you can. If you don't have any specific authentication needs, simply drop the jolokia.war into tomcat's /webapps directory. I suggest to try this first before adding security. For deinstalling the agent, simply remove the war.
As an alternative, you could also use the JVM agent, which opens an own HTTP server on an extra port (default: 8778). More on this in the reference manual
There is no need for a dedicated connection to the web app since MBeans are registered globally and are accesible from anywhere in the JVM. A webapp should of course select carefully the management information it exposes. So, there is no extra step needed and you can access the MBeans for the WEB app directly (except when it does something unusual with Java security, but I don't think so).
To test the installation, simply connect to the Tomcat with your browser and the context /jolokia (e.g. "http://localhost:8080/jolokia"). You should see the version information about the agent itself.
The next step would be to explore the JMX namespace, either with the browser (and operation "list" like in http://localhost:8080/jolokia/list , but that's tedious) or with a client like j4psh or hawt.io. Hopefully you will find the MBeans of your webapp you are looking for.

convert weblogic admin server into managed server

I'm currently having 2 Weblogic admin servers in 2 different domains created on the same machine.
I want to convert one of the admin server to a managed server and then use them together to deploy a Java application. Is this feasible? If yes, how?
I'm currently using Weblogic Server 10.3.
PS: I'm quite new to Weblogic domain creation and administration. Please revert for any more details needed.

The simple answer is no, however, adding a managed server to a domain is extremely simple. See the documentation here. When deploying your application you'll need to target both servers or create a cluster (also very easy), add both machines to it and give the cluster name as the target.
Note, it is generally not concidered best practice to target applications to the Admin server (although it's fine when you're developing on your local machine). If you have the resources available on your environment, you could create two managed servers and put them in a cluster. Depending on the configuration of your Admin server, you may be able to reduce it's size if memory is tight.

glassfish: remotely invoke EJB module with Application Client Container

After fighting passwords on Glassfish 4.x remotely on Ubuntu 14.04 Tahr, I'm ready to proceed to installing my first remote EJB module -- just want make sure I'm on the right path. Going from the Netbeans example Creating and Running an Application Client on the GlassFish Server, How would I make a client for the EJB module which is deployed remotely?
The Netbeans example assumes that Glassfish is running on the localhost. The exact mechanics are unclear to me, as it's not explicitly configured for localhost. Presumably it's implicitly configured for localhost...
I would like to use the ACC to connect to, not a local, but rather a remote Glassfish server. For context, the ACC is:
Introducing the Application Client Container
The Application Client Container (ACC) includes a set of Java classes,
libraries, and other files that are required for and distributed with
Java client programs that execute in their own Java Virtual Machine
(JVM). The ACC manages the execution of Java EE application client
components (application clients), which are used to access a variety
of Java EE services (such as JMS resources, EJB components, web
services, security, and so on.) from a JVM outside the Oracle
GlassFish Server. The ACC communicates with the GlassFish Server using
RMI-IIOP protocol and manages the details of RMI-IIOP communication
using the client ORB that is bundled with it. Compared to other Java
EE containers, the ACC is lightweight. For information about debugging
application clients, see Application Client Debugging.
GlassFish Server Open Source Edition Application Development Guide Release 4.0
see also:
https://stackoverflow.com/questions/25830149/how-to-package-a-stand-alone-remote-ejb-application-client
From a client application, how does the ACC remotely invoke the EJB module?
There must be a configuration. Does the ACC pick this up from jndi.properties? I can't find much documentation or examples on ACC usage. If the ACC is unsuitable, then, of course, I'll use a different approach. Presumably there's a way to specify a remote Glassfish server for the ACC.

How do you intend to deploy your application?
In my days when i use to develop application clients for the ACC, i used to bundle everything in an EAR (I will still do that, cause it is easier).
Glassfish deploys the artifacts, generates required configurations (You can override configurations in application.xml anyway).
One thing that the ACC takes care is the CORBA properties needed for remote connection.
When you download the client jar from the glassfish admin, you download a java webstart application, that downloads all required libraries as appropriate and a configuration is automatically set from which host (paramount that you set glassfish domain host properly, or this will be an internal IP or localhost) it was downloaded from.

Create a vendor-neutral EJB3 client

Is it possible to create a client that accesses an EJB3 bean, with the client having no dependence on a vendor JAR or configuration? We currently need to support scenarios where our service is deployed on a WebSphere or JBoss server, and the client is deployed as an application either on a WAS or JBoss, or is running as a standalone app.
I used to be able to do to this with EJB2.x beans, I just needed to create stubs using RMIC.
But with EJB3, If I'm connecting to WebSphere I have to include thinclient JARs, plus I have to pre-generate the stubs using WAS tools. For JBoss I have to use jboss-client.jar.

No, this is not possible. This has been made explicit in section 10 of the EJB 3.2 specification:
This chapter describes the interoperability support for accessing an
enterprise bean through the EJB 2.1 remote client view from clients
distributed over a network, and the distributed interoperability
requirements for invocations on enterprise beans from remote clients
that are Java Platform, Enterprise Edition (Java EE) components.
Distributed Interoperability is not defined for the EJB 3.x remote client view.
Also note section 10.5.5:
System value classes are serializable value classes implementing the
javax.ejb.Handle, javax.ejb.HomeHandle, javax.ejb.EJBMetaData,
java.util.Enumeration,java.util.Collection, and java.util.Iterator
interfaces. These value classes are provided by the EJB container
vendor. They must be provided in the form of a JAR file by the
container hosting the referenced bean. For interoperability scenarios,
if a referencing component would use such system value classes at
runtime, the Deployer must ensure that these system value classes
provided by the container hosting the referenced bean are available to
the referencing component. This may be done, for example, by including
these system value classes in the classpath of the referencing
container, or by deploying the system value classes with the
referencing component’s application by providing them to the
deployment tool.
For WebSphere Application Server, the EJB thinclient contains these system value classes as well as the IBM JNDI implementation that uses CosNaming. In theory, this thinclient is not needed if you don't need the system value classes and your client JVM has its own ORB with an implementation of CosNaming.

Short answer: No, it's not possible, as a client needs three things:
The interface classes.
The client libraries of the server AS (yes, sadly)
A configuration telling the client the server address/jndi lookup path (qa, prod etc.)
If your client is running on the same product (let's say JBoss to JBoss communication), you will not be in need of client libraries and just be able to do a remote lookup. If you have a mix of client/server application servers this will make things complicated, as you will have to run client libraries of one product in another server product.
Speaking of standalone applications running as clients, I'd just build and provide 1 heavy client jar/lib containing not only the interface classes, but also the client libs of both servers. Then providing a small helper class that returns the correct InitialContext created and based either on JBoss or Websphere depending on a flag in the client configuration.
I know this last idea ain't a clean solution, though might even work in a different AS product running as "client".

List all JNDI ports

Is that possible to find all open ports on my machine that were registered with JNDI ?
It would be good to find out some util from Ubuntu but Java code also will be OK.
UPDATE: After JSP's clarification I have revised my question.

I would do the following:
A. Parse your application server configuration - for example, for standalone configuration of Jboss AS 7.x , you should parse the standalone/configuration/standalone.xml
B. Read the JNDI configuration from the XML, and understand what ports should be used.
C. Use
System.getRuntime().exec
In order to invoke netstat -na , filter out those ports who exist in the list obtained from A, and that are in ESTABLISHED state.
Some issues wiht my solution:
A. As far as I know, According to Java EE spec, you should not execute process from a Java enterprise application.
To overcome this, you can have some j2se application running as service, communication with the application server.
B. I assumed that the server and the code that needs to know about the JNDI ports exist on the same machine.
If the code that needs to know the ports should be run on a different machine, you should expose this information to the client (i.e - via web UI, REST, etc...)