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CPT4 cpt.bat process issue

Vocabulary Users
#1

I have done many time updating the vocabulary and I didn’t have any issue, but this time.

vocabulary version V5.0 23-OCT-21

when I do the step to do “This utility will import the CPT4 vocabulary into concept.csv.” , looks like 312 concept get errored out.

[INFO ] 2021-10-26 09:17:29.015 [main] ConceptService - Writing updated data to CONCEPT.csv
Updated CPT4 records: 16615/16615
[INFO ] 2021-10-26 09:39:09.964 [main] ConceptService - Not processed cpt4 concepts: 312. See logs/not-processed-concepts-10-26-2021-09-17-27.out, file.

[INFO ] 2021-10-26 16:39:05.426 [main] ConceptService - Writing updated data to CONCEPT.csv
Updated CPT4 records: 312/312
[INFO ] 2021-10-26 16:41:25.550 [main] ConceptService - Not processed cpt4 concepts: 312. See logs/not-processed-concepts-10-26-2021-16-39-04.out, file.

I did vocabulary update 3 weeks ago with version v5.0 02-SEP-21 and the process completed successfully.
[INFO ] 2021-10-04 17:16:02.049 [main] ConceptService - Writing updated data to CONCEPT.csv
Updated CPT4 records: 16303/16303
[INFO ] 2021-10-04 17:37:54.608 [main] ConceptService - All cpt4 concepts are processed.

Thanks,

CPT4 Concept Processing Issue
Unable to process 312 v4 omop vocab concept codes within the april release
#2

Hi @shinjinaka ,
yes, you are right. Somehow the CPT4 tool seems to be behind with current versions, although we can confirm that the 312 new concepts in the recent release are actually present in UMLS. There is an Athena issue around this that I just updated. I think we will see a hot fix quite soon.

#3

@mik Thank you for the update. Please let me know when the hot fix goes in.

#4

It’s fixed!

#5

@Dymshyts I am still getting same error. Does the change apply immediately or
I need to wait a couple of days to get the change to be applied?

Thanks,

[INFO ] 2021-10-27 12:37:25.540 [main] ConceptService - Writing updated data to CONCEPT.csv
Updated CPT4 records: 16615/16615
[INFO ] 2021-10-27 12:59:14.777 [main] ConceptService - Not processed cpt4 concepts: 312. See logs/not-processed-concepts-10-27-2021-12-37-24.out, file. You can find more information about errors in the logs/logfile.log file

#6

You need to request the new vocabulary batch from the Athena.
Otherwise the archive you got the first time by that link is stored for a couple of days (so it wasn’t updated)

#7

@Dymshyts it worked. Thanks!

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