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Java error message when reconstitue CPT4

Vocabulary Users
#1

Hi folks,

I downloaded the vocabulary(full set) from athena.ohdsi.org today (April 22 version), and when I ran the commend, it threw out the message like this. The concept.csv file size was getting bigger that its original. Is it good or I have to concern?

Thanks,
Ray

I:\vocab>java -Dumls-apikey={my-umls-api} -jar cpt4.jar 5
[INFO ] 2022-05-03 19:37:05.530 [main] ConceptService - Writing updated data to CONCEPT.csv
Updated CPT4 records: 16615/16615
[INFO ] 2022-05-03 19:59:41.197 [main] ConceptService - All cpt4 concepts are processed.
Exception in thread ā€œmainā€ org.odhsi.utils.cpt.Cpt4Exception: Unexpected code Response{protocol=http/1.1, code=401, message=Unauthorized, url=https://utslogin.nlm.nih.gov//cas/v1/tickets/TGT-406393-u3vqv19bkl2qwstfg-cas}
at org.odhsi.utils.cpt.restclient.RestTicketClient.checkSuccessful(RestTicketClient.java:76)
at org.odhsi.utils.cpt.restclient.RestTicketClient.logout(RestTicketClient.java:113)
at org.odhsi.utils.cpt.restclient.RestTicketClient.close(RestTicketClient.java:125)
at org.odhsi.utils.cpt.Application.main(Application.java:49)

Cpt4.sh not working
#2

The cpt4.jar add the concept name (description) to concept.csv, so it is likely to get larger. Is there an addition information in logs/logfile.log?

#3

Hi Don,

I donā€™t see error or exception message in the logfile.

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#4

I would go ahead with loading the vocabulary. Maybe someone more familiar with the cpt4.jar code can tell you more about the errors you got.

#5

Alright. Thank you very much Don!

Ray

#6

Hi Guys:
I got the same error as well. but it raised the exception after the CPT4 was extracted.

#7

Please open ticket in Athena GitHub

#8

I have created an Athena issue. From what we see, the CPT4 reconstitution is however still complete, so we can keep using the cpt4.jar executable for the time being. Apparently the API call needs to be adjusted to a changed API definition on UMLS side.

#9

Did anyone found the solution for this error? I am facing same issue while running cpt4 jar file?

#10

Hi @Siddhesh_3012 , right now it seems the described error messages do not indicate that the cpt4.jar function of adding concept names to the vocabulary csvā€™s is actually impaired. We suspect there is some issue when closing the API connection, but it will take a while until this is fixed.

#11

Hello all,

Was not sure if I needed to submit a separate topic and Athena issue, but I tried a download and CPT4 reconstitution yesterday (2022-07-20) and am getting a similar exception:

java -Dumls-apikey= -jar cpt4.jar 5
[INFO ] 2022-07-21 10:25:26.999 [main] ConceptService - Writing updated data to CONCEPT.csv
Updated CPT4 records: 16615/16615
[INFO ] 2022-07-21 10:36:02.486 [main] ConceptService - All cpt4 concepts are processed.
Exception in thread ā€œmainā€ org.odhsi.utils.cpt.Cpt4Exception: Unexpected code Response{protocol=h2, code=401, message=, url=https://utslogin.nlm.nih.gov//cas/v1/tickets/TGT-28457-ehrwe4wtl5v4lf6m-cas}
at org.odhsi.utils.cpt.restclient.RestTicketClient.checkSuccessful(RestTicketClient.java:76)
at org.odhsi.utils.cpt.restclient.RestTicketClient.logout(RestTicketClient.java:113)
at org.odhsi.utils.cpt.restclient.RestTicketClient.close(RestTicketClient.java:125)
at org.odhsi.utils.cpt.Application.main(Application.java:49)

Except for me, none of the CPT4 concept IDs are in the CONCEPT.csv file afterwards.

Has there been any development in this issue since the last post?

#12

Hi @rsanka - Did you check your logfile? (logs/logfile.log)
Last time we checked, the cpt4.jar still does work.
The message ā€œUpdated CPT4 recordsā€ actually looks quite promising.
~Mik

#13

Hmm, the logfile shows only SUCCESS lines.

So, could there be an error after the concept processing, but before the changes are saved to CONCEPT.csv?

#14

Huh, ran the script a second time and the CONCEPT.csv now has the CPT4 concept IDs.

Maybe I made a mistake when I first checked, but looks like itā€™s working as you said @mik. Thanks!

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