OHDSI Home | Forums | Wiki | Github

Error when Generating Cohort (SQL query not fully formed)


We have an instance of ATLAS and get an error when generating a cohort (this is using SYNPUF5). Interestingly, or oddly, the table in the error message is pointing to the RESULTS schema when I was expecting it to point to the OHDSI schema, where the COHORT_INCLUSION table exists (but does not get populated). Obviously we have some wires crossed.

"java.lang.RuntimeException: org.springframework.jdbc.BadSqlGrammarException:
PreparedStatementCallback; bad SQL grammar [DELETE FROM RESULTS.cohort_inclusion WHERE cohort_definition_id = ?;];
nested exception is java.sql.SQLSyntaxErrorException: ORA-00933: SQL command not properly ended

Any hints on how to debug this? Thanks, Jeff

(Seng Chan You) #2

Could you tell us which SQL you use? (sql server? oracle? or ?)

(Chris Knoll) #3

Looks like oracle, and looks like the trailing ; is the problem. We’ll have to find the part of code that is executing that statement.

@jeffmillstein, could you open an issue on the webapi repo: github.com/ohdsi/webapi?


Thanks @Chris_Knoll. (We are running on Oracle rds 12c). We’re looking to see if we can find were this query is generated. I’ll enter a bug report today. Thanks, Jeff