Cpt4 utility not working

Implementers
1

I am trying to run the cpt4 utility to update the CONCEPT table but I am running into an issue. One thing I did notice is that there was no lib folder in my download. Here is the error I am receiving:

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Exception in thread “main” java.lang.NoClassDefFoundError: javax/xml/ws/Service
at java.base/java.lang.ClassLoader.defineClass1(Native Method)
at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1016)
at java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:151)
at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:821)
at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:719)
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:642)
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:600)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
at org.odhsi.utils.cpt.ApplicationContextServer.init(ApplicationContextServer.java:42)
at org.odhsi.utils.cpt.Application.main(Application.java:44)
Caused by: java.lang.ClassNotFoundException: javax.xml.ws.Service
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:602)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
… 11 more

Thanks in advance…

2

Hello @oksanascott,

This is only a warning, so it shouldn’t prevent the utility from working completely. Were there any other errors?
Also, if it’s possible, you could try using Java 8 to run this.

3

Thanks for the reply. According to the logfile, the update failed:

[INFO ] 2019-11-15 08:19:10.380 [main] Application - Update failed. Usage: java -Dumls-user= -Dumls-password= -jar cpt4.jar
-Dumls-user is mandatory.
-Dumls-password is mandatory.
version is mandatory. Possible values are 4 or 5
output-file-name is optional.

I will try installing Java 8 and re-running.
Thanks!

4

I re-ran using Java 8 and I get the same error. I downloaded the vocabularies 3 times and never got a lib folder with the downloads. It looks like maybe a java.xm.ws file is missing?

5

I was able to resolve the java.lang.NoClassDefFoundError: javax/xml/ws/Service by using Java 8 and making sure my JAVA_HOME was correct (I use jenv).

I then ran:

./cpt.sh USERNAME PASSWORD

However, my password has a $ in it, so I had to escape it. My command ended up looking something like:

./cpt.sh username “pa\$\$word”

@oksanascott, what command did you run, and which error did you see again?

EDIT: The same issue is also discussed here:

6

I’m using Windows 10. I installed Java 8 and updated the PATH and JAVA_HOME variables.
I ran: java -Dumls-user=xxx -Dumls-password=xxx -jar cpt4.jar 5

My password has an ‘@’ in it, does it need to be escaped?

7

I’m not sure if @ needs to be escaped, but it might be worth trying using quotes:

java -Dumls-user=“xxx” -Dumls-password=“xxx” -jar cpt4.jar 5

and escaping:

java -Dumls-user=“xxx” -Dumls-password=“x\@xx” -jar cpt4.jar 5

Can you share the full output that you are seeing, as well as the contents of the log file here?

Also, what does running the following show?

java -version

8

I got it to work. I uninstalled Java 13 and installed Java 8 and then it worked. Just an FYI, I didn’t need to escape the ‘@’ in my password.

Thank you for all your help!

1 Like
9

@Chris_Knoll, @Christian_Reich

How to make the cpt4.jar file run with latest version of Java? I don’t have java8 on the machine.

10

Hi CSC,
Сurrently only java version 8 is supported. Support for higher versions will be added in the next version.

11

Assuming you have Docker installed, one simple solution is to navigate to the directory containing cpt.sh and then run:

docker run --rm -v ${PWD}:/ohdsi -w /ohdsi openjdk:8u232-jre ./cpt.sh user pass

Replacing user and pass with your UMLS credentials.

12

Any idea when the next version will be released to support later versions of Java?