OHDSI Home | Forums | Wiki | Github

CPT4.bat only extracts about half of CPT4 concepts. Others fail and no error message is given

I’m having an issue similar to:

I just download a new vocabulary zip from https://athena.ohdsi.org.

When I run cpt4.bat I get about half of the concepts but the other half fail. There doesn’t appear to be any error message in the log file.

The log file and not processed concepts file are attached below.
logfile.log.txt (2.4 MB)
not-processed-concepts-08-05-2023-08-25-11.out.txt (773.0 KB)

Dear @greshje.gmail

Thank you for reporting this We are investigating this issue.

1 Like

There is an issue logged on GitHub:

1 Like

UPD: it was a temporal issue on the UMLS side.

Everything should work fine now.

1 Like

I just did a fresh download and I’m still getting 13367 concepts not processed (running on Windows)

This is also failing using Java 11.

It looks like this might be UMLS limiting the number of requests per time-unit (hour?). Fortunately cpt4.bat can be run incrementally (it will only query for concepts that have not already been processed).

On the first run, 7,693 concepts failed to process. Re-running immediately, the same 7,693 concepts failed. Running about 2 hours later all of the remaining 7,693 concepts processes successfully.

See screen shot below: