Unable to process 312 cpt4 code for omop vocab V4 april release data but there is no issue in V5 vocab data.
Did anyone face similar issues with the V4 vocab data?
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I had a similar problem. Seems there where connection problems running the cpt4.jar. To resolve I got the concept ids from the cpt4.jar error log and then wrote SQL to insert into v4.concept getting the information from the v5 concept table.
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Hi there,
we have a github issue for Don’s finding and a more general one as well as an older forum thread.
Bottom line is: the v5 download contains a patched cpt4.jar file while the v4 download does not. A simpler approach than what Don has been doing is to download a v5 vocab file with only the CPT4 vocabulary checkbox marked for downloading. Then take the cpt4.jar file from this download and copy it over to your extracted v4 vocabulary folder to replace the one that came with it.
Thank you Michael.
Providing an update of further advises from Michael, as would be useful for others encountering similar issues -
Executed the below steps-
The below are the steps that I have done, as per what I understood, please correct me if there is anything wrong –
- I selected only the CPT4 vocab from the athena.org and selected V5, downloaded
- From the (1), I took only the cpt4.jar and replaced it in the version 4 folder (already downloaded folder).
- Re-ran the cpt4.jar, it processed only the 312 records and did not error but threw out another cpt4exception
- I checked the log files for the current date, the records are marked as ‘SUCCESS’.
Can we confirm if my records are correctly processed? Kindly advise.
cpt4 exception encountered is as attached -
Reply from Michael on the above exception -
"I just, very recently ran the cpt4.jar and encountered the same error messages. If I interpret them correctly, the concept.csv has been successfully updated. I checked the file and the lines for CPT4 vocabulary concepts have a concept_name so it looks good.
My assumption is that UMLS has slightly changed their API and that the exceptions we are seeing result from the CPT4.jar API call not being adapted to the latest version of the UMLS API".
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