Protege Server don`t load the JDBC driver

[zullyvan]

Hi
I was testing the Muti-User OpenSource installation, but, I have an error when the Protege server was loading de driver for connect the database, this is te error:

WARNING: org/postgresql/Driver : Unsupported major.minor version 52.0 -- java.lang.UnsupportedClassVersionError: org/postgresql/Driver : Unsupported major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(Unknown Source)
. . .

I probed different versions of the driver, but neither was successfull. How I need to do?

[neil.walsh]

That sounds like a Java version mismatch. Can I confirm you are using Java 8 and a Java 8 compatible JDBC driver?

[zullyvan]

Hi,

This my Java version

java version "1.8.0_441"
Java(TM) SE Runtime Environment (build 1.8.0_441-b07)
Java HotSpot(TM) 64-Bit Server VM (build 25.441-b07, mixed mode)

I tested the versions of JDBC Driver in this page (version 42.7.5, 42.7.4 both for Java 8)

https://jdbc.postgresql.org/download/

Verion of the data base postgresql:
postgres (PostgreSQL) 17.2

What other validations you suggest that I can do?

this is the first error:

WARNING: org/postgresql/Driver : Unsupported major.minor version 52.0 -- java.lang.UnsupportedClassVersionError: org/postgresql/Driver : Unsupported major.minor version 52.0

the second error:
WARNING: Unable to load knowledgebase jdbc:postgresql://localhost:5432/essentialdb -- java.lang.RuntimeException: class not found: org.postgresql.Driver

Aditional, I have this error in the RMI window:

Could not set up class specific logging
Exception configuring logger
Could not set logger level
Warning: IO exception getting logger. access denied (java.util.PropertyPermission protege.properties.in.user.home read)

[neil.walsh]

The second issue looks like a permissions problem writing logs to the Protege logs folder in the Protege installation folder. If you are using Linux, then you can use

Code: Select all

ls -la

to review

Code: Select all

chmod

to set the correct permissions.

I'm guessing you are using I've just noticed our download page was hosting an incorrect version of Protege (now fixed). The version that was there had an older pre-packaged version of Java which may be causing this issue.

You can either remove you Protege install and reinstall this version:
Windows
https://cdn.enterprise-architecture.org ... -noJVM.exe
Linux
https://cdn.enterprise-architecture.org ... -noJVM.bin
macOS
https://cdn.enterprise-architecture.org ... MacOSX.zip


....or you can modify the startup script to point to your Java 8 installation.

When starting Protege, you should see a line something line this:

Code: Select all

Protege 3.5 Build 663, JVM 1.8.0_332-b09, memory=1908M, Mac OS X, encoding=UTF-8, language=en, country=GB

Let me know how you get on

[zullyvan]

Hi,

I'm trying to install it on a Windows 10.

You're right I was trying with a installer with the VM inside and that VM is in Java 6.
But I need to work on Java 8.

I tried to change the file run_protege_server.bat
changing this line:
set JDKBIN=jre\bin

to:
set JDKBIN="C:\Program Files\Java\jre1.8.0_441\bin"

but when I try to run the server (run_protege_server.bat) I have an error that not recognize the Java Command

In the other option, I downloaded the installer that you mention, without the VM inside, but I have different mistakes when I try to install it:

An error:
Flexeraawy$aaa: Windows DLL failed to load
at Flexeraawy.af(Unknown Source)
at Flexeraawy.aa(Unknown Source)
at com.zerog.ia.installer.LifeCycleManager.init(Unknown Source)
at com.zerog.ia.installer.LifeCycleManager.executeApplication(Unknown Source)
at com.zerog.ia.installer.Main.main(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.zerog.lax.LAX.launch(Unknown Source)
at com.zerog.lax.LAX.main(Unknown Source)

then, I change different values in the system variables:

CLASSPATH=C:\Program Files\Java\jre1.8.0_441\lib
JAVA_HOME=C:\Program Files\Java\jre1.8.0_441
JAVA_TOOL_OPTIONS=-Dos.name=Windows Server 2016
JDK_HOME=%JAVA_HOME%
JRE_HOME=%JAVA_HOME%\jre
Path=Other values...;C:\Program Files\Java\jre1.8.0_441\bin

Other error:
When I put this values and try to install it, I have this error in an emergent window:

Title in the label of the emergent window: Java Virtual Machine Launcher
Error: Could not create the Java Virtual Machine.
Error: A fatal Exception has occurred. Program will exit.

What other options to resolve these problems you'll suggest?

Protege 3.5 is the correct version that I need to install?
Protege 3.5 is a version available for Java 8?
Protege 3.5 is only available for Linux?
Exists an installer version for Protege 3.5 with Java 8 inside?

[zullyvan]

Hi

Please, I've my hopes in this Open Source tool (Multi-User).

Any advice or option?

Maybe a Docker with the Protege Server?

[terry]

You can follow this path to have a entire Essential Open Source version running using Docker.

viewtopic.php?f=21&t=3086

Just ignore "Deploy on Azure" steps if you want.

[neil.walsh]

Hi,

I'm going to see if I can recreate this. I don't have a Windows installation to hand but I'll get something setup and get back to you as quickly as possible. Apologies for the delay, we've been working on a new release and it has occupied a lot of resources within the company over the past few weeks.

Best,

Neil

[neil.walsh]

Hi,

I've been able to replicate your issues and have a workaround I believe should work. I'll log a ticket internally to rectify this properly but hopefully the steps below should get you moving again.

Firstly, check you have Java 8 (1.8) installed, added to your PATH and your JAVA_HOME set. I think you have this already.

Next, Install Protege using the version with the included JVM. This is the version currently on our site as I write this. We will not be using this JVM but the installer for this version works properly. It may ask you to select your JVM during the install. You will still need to perform the steps below.

Once installed, navigate to the installation folder, e.g.

Code: Select all

"C:\Program Files\Protege 3.5\"

Edit the file called run_protege.bat as administrator in a text editor of your choice

Modify the line that starts "set JAVA_PATH = ..." to point to the "bin" folder of your Java installation. For example:

Code: Select all

set JAVA_PATH="C:\Program Files\Zulu\zulu-8\bin"

Whilst you are here, set the MAXIMUM_MEMORY to 2048M

Next, modify the run_protege_server.bat file, this time updating the line that starts "set JDKBIN=..." to point to the "bin" folder of your Java install.

Again, whilst you are here, set the MAX_MEMORY to 2048M

Now, running Protege, it will utilise the Java 8 install. You should see this reflected in the command line output.

Let me know if this helps

Best,

Neil

[zullyvan]

You can follow this path to have a entire Essential Open Source version running using Docker.

viewtopic.php?f=21&t=3086

Just ignore "Deploy on Azure" steps if you want.

Thanks,

I was trying to develop it in a docker desktop in Windows, but I have two errors when the containers (protege & viewer) try to run:

viewer-1 | exec /usr/local/bin/startup.sh: no such file or directory
protege-1 | /__cacert_entrypoint.sh: line 114: /opt/run_protege.sh: cannot execute: required file not found

How can I do to solve these errors?

[zullyvan]

Hi,

I've been able to replicate your issues and have a workaround I believe should work. I'll log a ticket internally to rectify this properly but hopefully the steps below should get you moving again.

Firstly, check you have Java 8 (1.8) installed, added to your PATH and your JAVA_HOME set. I think you have this already.

Next, Install Protege using the version with the included JVM. This is the version currently on our site as I write this. We will not be using this JVM but the installer for this version works properly. It may ask you to select your JVM during the install. You will still need to perform the steps below.

Once installed, navigate to the installation folder, e.g.

Code: Select all

"C:\Program Files\Protege 3.5\"

Edit the file called run_protege.bat as administrator in a text editor of your choice

Modify the line that starts "set JAVA_PATH = ..." to point to the "bin" folder of your Java installation. For example:

Code: Select all

set JAVA_PATH="C:\Program Files\Zulu\zulu-8\bin"

Whilst you are here, set the MAXIMUM_MEMORY to 2048M

Next, modify the run_protege_server.bat file, this time updating the line that starts "set JDKBIN=..." to point to the "bin" folder of your Java install.

Again, whilst you are here, set the MAX_MEMORY to 2048M

Now, running Protege, it will utilise the Java 8 install. You should see this reflected in the command line output.

Let me know if this helps

Best,

Neil

Thanks
I did that changes, but appear this error:

Loading project plugins for project essential_baseline_6_19
SEVERE: java.rmi.ServerException: RemoteException occurred in server thread; nested exception is:
java.rmi.UnmarshalException: error unmarshalling arguments; nested exception is:
java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server_Stub
at sun.rmi.server.UnicastServerRef.dispatch(Unknown Source)
at sun.rmi.transport.Transport$1.run(Unknown Source)
at sun.rmi.transport.Transport$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at sun.rmi.transport.Transport.serviceCall(Unknown Source)
at sun.rmi.transport.tcp.TCPTransport.handleMessages(Unknown Source)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(Unknown Source)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$0(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
at sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(Unknown Source)
at sun.rmi.transport.StreamRemoteCall.executeCall(Unknown Source)
at sun.rmi.server.UnicastRef.invoke(Unknown Source)
at sun.rmi.registry.RegistryImpl_Stub.rebind(Unknown Source)
at edu.stanford.smi.protege.server.Server.bindName(Unknown Source)
at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
at edu.stanford.smi.protege.server.Server.main(Unknown Source)

According to other questions in the forum where appear this error, I set in the run_protege_server.bat file this line:

set CODEBASE_URL="http://localhost:8080/essential_viewer/protege.jar"

and copy the protege.jar to the viewer folder

C:\Program Files\Apache Software Foundation\Tomcat 9.0\webapps\essential_viewer

but, I have the same error
Any suggestion?

[neil.walsh]

Hi,

The codebase URL needs to be formatted as a URL. Can you try setting your codebase URL to the following:

Code: Select all

set CODEBASE_URL=file:/c:/program%20files/protege_3.5/protege.jar

[terry]

You can follow this path to have a entire Essential Open Source version running using Docker.

viewtopic.php?f=21&t=3086

Just ignore "Deploy on Azure" steps if you want.

Thanks,

I was trying to develop it in a docker desktop in Windows, but I have two errors when the containers (protege & viewer) try to run:

viewer-1 | exec /usr/local/bin/startup.sh: no such file or directory
protege-1 | /__cacert_entrypoint.sh: line 114: /opt/run_protege.sh: cannot execute: required file not found

How can I do to solve these errors?

The issue occurs because you are using a Windows environment, which means the files have line breaks in CRLF (Windows) format instead of LF (Linux). This prevents the Linux shell from interpreting them correctly.

To fix this, run the following commands in your repository before starting the container:

Code: Select all

git config --global core.autocrlf input
git rm --cached -r .
git reset --hard

Since I needed to test this solution, I added a PowerShell script to the repository that automatically applies this configuration. You can run it with:

Code: Select all

EssentialOpen> powershell -File scripts_win\1_prepare.ps1

If everything is correct, the docker compose up command should now work properly. Let me know if it works for you or if you encounter any other issues!