Cohort Generation in Atlas with Generation status Failed

psbrandt · November 18, 2019, 10:16pm

The issue is that the tables are created by the Flyway migrations. So, the cohort_inclusion_result table is created as follows:

github.com

OHDSI/WebAPI/blob/e81004901b3ead77f426c72cf07db6a6a195ea03/src/main/resources/db/migration/postgresql/V1.0.2.0__cohort_feasiblity.sql#L9-L14


      
          CREATE TABLE ${ohdsiSchema}.cohort_inclusion_result(
            cohort_definition_id int NOT NULL,
            inclusion_rule_mask bigint NOT NULL,
            person_count bigint NOT NULL
          )
          ;

Note the missing mode_id column. The same is true for the cohort_inclusion_stats and cohort_summary_stats tables.

The v2.5.0 release contains instructions on how to manually resolve the issue, but a Flyway migration was not included to automate this schema change. One possible solution is to provide a Flyway migration that brings the schema up to date, which is what I’ve done here.

For convenience, in Postgres, the solution is to run the following:

ALTER TABLE @resultsSchema.cohort_inclusion_result ADD mode_id  int NOT NULL DEFAULT 0;
ALTER TABLE @resultsSchema.cohort_inclusion_stats ADD mode_id  int NOT NULL DEFAULT 0;
ALTER TABLE @resultsSchema.cohort_summary_stats ADD mode_id  int NOT NULL DEFAULT 0;

where @resultsSchema is the name of the schema containing the WebAPI tables.