OHDSI Home | Forums | Wiki | Github

Import from AWS yields errors in vocabulary query

Developers
#1

Part of our project is to get Atlas running on Kubernetes, and launchable per student (each student will have their own) we has taken to import the ohdsi-in-a-box databases from AWS as an initial approach and have beeen largely successful. with one exception.

Selecting the “Configuration” LHS button, yeilds an error in the webapi.

2022-11-07 21:50:53.979 ERROR http-nio-8080-exec-11 org.ohdsi.webapi.util.GenericExceptionMapper - [] - org.springframework.dao.IncorrectResultSizeDataAccessException: Incorrect result size: expected 1, actual 2
    at org.springframework.dao.support.DataAccessUtils.requiredSingleResult(DataAccessUtils.java:72)
    at org.springframework.jdbc.core.JdbcTemplate.queryForObject(JdbcTemplate.java:799)
    at org.ohdsi.webapi.service.VocabularyService.getInfo(VocabularyService.java:1194)

Which can be found here

this is could be misconfiguration on our part

#2

Hello @Jeff_Waller,

Is it possible that Vocabulary table has two rows with vocabulary_id = 'None'? This query is supposed to always return a single row that contains OMOP Vocabulary package version.

#3

Hi @rookie_crewkie ,
No, it is not, since the vocabulary_id is a primary key in the vocabulary table. I mean, if you have more than one record with the same vocabulary id in the vocabulary table it is not correct.

#4

Can you check this? because @rookie_crewkie is correct that the query that threw the exception is simply:

select VOCABULARY_VERSION 
from @CDM_schema.vocabulary
where VOCABULARY_ID = 'None'

Can you run this query on your database and see what rows you get? Maybe you don’t have the primary keys applied…

#5

I did find that there were multiple entries in the vocabulary table as a result of an incorrect database import. Fixing the import fixed the problem.

1 Like
t