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OHDSI / ETL-CMS

Workproducts to ETL CMS datasets into OMOP Common Data Model
Apache License 2.0
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Update readme file for CPT VOCAB append #41

Closed vickysam closed 2 months ago

vickysam commented 7 years ago

File to update : https://github.com/OHDSI/ETL-CMS/blob/master/python_etl/README.md#3-download-cdmv5-vocabulary-files

Currently command to append CPT4 is:

java -jar cpt4.jar

It should be:

java -jar cpt4.jar <version = 4 or 5>

cgreich commented 7 years ago

Will fix. Thanks, @vickysam.

topspinj commented 5 years ago

Athena instructions require you to pass in username and password of your UMLS account: 

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

Can you run it without?

topspinj commented 5 years ago

I get the following error when I run java -jar cpt4.jar 5: 

Error: Unable to initialize main class org.odhsi.utils.cpt.Application
Caused by: java.lang.NoClassDefFoundError: javax/xml/ws/WebServiceException

using Java v11. I'm not very familiar with Java, do you know what the issue might be?

cgreich commented 5 years ago

No, you need to have your UMLS license and credentials. The machine needs access to the internet. Without any proxy gymnastics. Does it?

topspinj commented 5 years ago

Am still seeing that error (above) when I pass in my UMLS credentials.

topspinj commented 5 years ago

Update: The jar file isn't compatible with Java 11. After downgrading Java, I no longer get the error above.

I think it would be useful to update the docs:

  1. specify which Java version to use (version 10 or lower)
  2. add UMLS credentials to jar command java -Dumls-user=xxx -Dumls-password=xxx -jar cpt4.jar <version = 4 or 5> (or just use bash cpt.sh)