Trying to set up OMOP dataset in i2b2-pg to test out the act-omop project feature. Followed all instructions per this link:
https://community.i2b2.org/wiki/display/getstarted/i2b2-on-OMOP+With+ENACT-OMOP+Ontology+v4.1
I'm able to login as demo and the UI comes up with the proper ACT-OMOP folders. When I run a search, I get an error. The Wildfly logs have this error:
2025-02-27 19:55:23,440 ERROR [edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorHelperDao] (Thread-278) [EVENT UNSPECIFIED Anonymous:@unknown -> /ExampleApplication/edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorHelperDao] Error while executing sqlinsert into QUERY_GLOBAL_TEMP (patient_num, panel_count)_with t as ( _ select f.patient_num _from i2b2demodata.observation_fact f _where _f.EMPTY_VIEW.CONCEPT_CD IN (select EMPTY_VIEW.CONCEPT_CD from i2b2demodata.concept_dimension where concept_path LIKE '\ACT\Diagnosis\ICD9\V2_2018AA\A18090800\A8359006\A8359307\A15573936\A8352361%') _group by f.patient_num _ ) _select t.patient_num, 0 as panel_count from t org.postgresql.util.PSQLException: ERROR: missing FROM-clause entry for table "empty_view" Position: 177
There are extra '_' characters in the SQL, and EMPTY_VIEW is appended where it's not needed. Looks like a configuration step in postgre/wildfly/webclient has been omitted for querying OMOP data in the instructions?
Trying to set up OMOP dataset in i2b2-pg to test out the act-omop project feature. Followed all instructions per this link:
https://community.i2b2.org/wiki/display/getstarted/i2b2-on-OMOP+With+ENACT-OMOP+Ontology+v4.1
I'm able to login as demo and the UI comes up with the proper ACT-OMOP folders. When I run a search, I get an error. The Wildfly logs have this error:
2025-02-27 19:55:23,440 ERROR [edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorHelperDao] (Thread-278) [EVENT UNSPECIFIED Anonymous:@unknown -> /ExampleApplication/edu.harvard.i2b2.crc.dao.setfinder.QueryExecutorHelperDao] Error while executing sqlinsert into QUERY_GLOBAL_TEMP (patient_num, panel_count)_with t as ( _ select f.patient_num _from i2b2demodata.observation_fact f _where _f.EMPTY_VIEW.CONCEPT_CD IN (select EMPTY_VIEW.CONCEPT_CD from i2b2demodata.concept_dimension where concept_path LIKE '\ACT\Diagnosis\ICD9\V2_2018AA\A18090800\A8359006\A8359307\A15573936\A8352361%') _group by f.patient_num _ ) _select t.patient_num, 0 as panel_count from t org.postgresql.util.PSQLException: ERROR: missing FROM-clause entry for table "empty_view" Position: 177
There are extra '_' characters in the SQL, and EMPTY_VIEW is appended where it's not needed. Looks like a configuration step in postgre/wildfly/webclient has been omitted for querying OMOP data in the instructions?