I’m having the same problem. I tried to walk around this issue by using CPT4 concept that I previously downloaded in Sep 2022 but it failed.
SQL Error [23503]: ERROR: insert or update on table “concept_relationship” violates foreign key constraint “fpk_concept_relationship_c_1”
Detail: Key (concept_id_1)=(777313) is not present in table “concept”.
Looking at the Athena last update for CPT4, it shows “01-May-2022”, but Athena has Valid start “12-Oct-2022”. so we have new CPT4 version in Athena? @mik @Dymshyts Could you fix the issue like you did last year? Thanks.
Our engineers have run into the same problem. I can’t tell from the threads if there’s a fix available or whether we should use old tables instead. @Christian_Reich?
Hi @david_seligman , do you reference to " violates foreign key "? If that is the case, you are trying to mix vocabulary versions in your tables. When loading vocabularies clear your vocabulary tables first and load them fresh…
If you are experiencing issues with operating the cpt4.jar, we have just noticed that we need to finetune that again for the latest release. Bear with us a little.
@mik Thank you. This is the error we got “2022-12-06 00:18:10.517 [main] ConceptService - Not processed cpt4 concepts: 12714. See logs/not-processed-concepts-12-05-2022-22-13-43.out, file.” We can post the log file if it would be helpful.
okay, @david_seligman , sounds like you need the fixed cpt4.jar. We are currently testing it and I will post here, once it is available through ATHENA. You will have to re-initiate the vocabulary download (go to the download page, select your vocabs and request the download). My assumption is that it should be available tomorrow (stay tuned).
There are some obstacles that will need more time to address them. The tool will be updated on Monday.
The new version of CPT4 tool was published in ATHENA.
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Thank @Konstantin_Yaroshove for the update. I tested rerunning the process after the new release and did not encounter any issues.
I found the update took some time to do (around 4-5 hours). Is this expected?
Many thanks,
Solmaz
@solmaz.eradat Yes, it’s expected. Unfortunately, this limitation comes from UMLS side.
We are looking for possible solutions to improve the speed.
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After the recent CPT4 update, we were updating our vocabulary tables using the scripts in the DDL folder https://github.com/OHDSI/CommonDataModel/blob/main/inst/ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_constraints.sql.
An error was generated when running line 319 https://github.com/OHDSI/CommonDataModel/blob/main/inst/ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_constraints.sql#L319
It seems the following concept_ids:
- 45889325
- 45890303
are not in the concept table.
Checked on the Athena website and these ids are coming from the CPT4 vocab.
The fields and tables below are the once be effected:
many thanks,
Solmaz
Hi @solmaz.eradat ,
I checked my csv files and found the concept id 45889325 and 45890303 in both, the CONCEPT_CPT4 and the CONCEPT.csv file after reconstitution. As tiresome it is, can you re-run the download and reconstitution exercise if you cannot find those id’s in your csv files? If you do find them, there must be something happening during the import.
cheers - mik
Hi @mik . Thanks for the suggestion. Reran the steps again with a fresh Athena download and cpt run and no issues this time. Thanks.
I am facing the same issue with the latest cpt4.jar that comes with the vocabulary download where a large no of concept update is failing. Tried looking for the source code but couldn’t find it. By any chance, is the cpt4.jar source code available on Ohdsi git?
I downloaded OMOP vocabulary with version v5.0 31-AUG-23 two weeks ago and ran into the same issue with cpt4.jar. Lots of not processed cpt4 concepts.
Try running the cpt4 load program again, in the same directory. I found that on the first pass it failed to load a large number of CPT4 codes, but then running it again, the program somehow knew what codes failed to load and it updated just those coded.
Thanks, @DTorok
I have run the cpt4 few times, it looks like all the CPT 4 concepts got updated.
Jack
This issues still persist in 6/7/2024. out of the 17k Cpt4 codes around 3k gets loaded in. Vocabulary was downloaded on 6/4/2024 using version 5.
Still encountering this issue as well with the latest 20240830 vocabulary (9/9/2024). Started with ~17k CPT4 codes, then we run it multiple times, each time lowering the number of unprocessed concepts.
13576
13561
2208
1350
1325
… still going