OHDSI / CohortDiagnostics

An R package for performing various cohort diagnostics.
https://ohdsi.github.io/CohortDiagnostics
41 stars 48 forks source link

Error in `cohort_relationships` when migrating data model #1139

Closed anthonysena closed 4 days ago

anthonysena commented 1 week ago

Changes in #1135 removed columns from cohort_relationships which then causes migration inst/sql/sql_server/migrations/Migration_5-v3_3_0_remove_overlap_table.sql to fail (see below).

Migrating data set
Migrator using SQL files in CohortDiagnostics
Connecting using PostgreSQL driver
Creating migrations table
  |======================================================================| 100%
Executing SQL took 0.0314 secs
Migrations table created
Executing migration: Migration_1-v3_1_0_time_id.sql
  |======================================================================| 100%
Executing SQL took 0.0237 secs
Saving migration: Migration_1-v3_1_0_time_id.sql
  |======================================================================| 100%
Executing SQL took 0.00723 secs
Migration complete Migration_1-v3_1_0_time_id.sql
Executing migration: Migration_2-v3_1_0_ir_person_years.sql
  |======================================================================| 100%
Executing SQL took 0.0244 secs
Saving migration: Migration_2-v3_1_0_ir_person_years.sql
  |======================================================================| 100%
Executing SQL took 0.00543 secs
Migration complete Migration_2-v3_1_0_ir_person_years.sql
Executing migration: Migration_3-v3_2_0_suport_cohort_subsets.sql
  |======================================================================| 100%
Executing SQL took 0.0257 secs
Saving migration: Migration_3-v3_2_0_suport_cohort_subsets.sql
  |======================================================================| 100%
Executing SQL took 0.00565 secs
Migration complete Migration_3-v3_2_0_suport_cohort_subsets.sql
Executing migration: Migration_4-v3_2_1_cohort_name_field.sql
  |======================================================================| 100%
Executing SQL took 0.00528 secs
Saving migration: Migration_4-v3_2_1_cohort_name_field.sql
  |======================================================================| 100%
Executing SQL took 0.00482 secs
Migration complete Migration_4-v3_2_1_cohort_name_field.sql
Executing migration: Migration_5-v3_3_0_remove_overlap_table.sql
Closing database connection
  |======================================================================| 100%
Executing SQL took 0.00463 secs
Error in value[[3L]](cond) : 
  DROP TABLE IF EXISTS results.cd_cohort_overlap;
ALTER TABLE results.cd_cohort_relationships DROP COLUMN rec_cs_before_ts;
ALTER TABLE results.cd_cohort_relationships DROP COLUMN rec_cs_on_ts;
ALTER TABLE results.cd_cohort_relationships DROP COLUMN rec_cs_after_ts;
ALTER TABLE results.cd_cohort_relationships DROP COLUMN rec_cs_before_te;
ALTER TABLE results.cd_cohort_relationships DROP COLUMN rec_cs_on_te;
ALTER TABLE results.cd_cohort_relationships DROP COLUMN rec_cs_after_te;
ALTER TABLE results.cd_cohort_relationships DROP COLUMN rec_cs_window_t;
ALTER TABLE results.cd_cohort_relationships DROP COLUMN rec_ce_window_t;
ALTER TABLE results.cd_cohort_relationships DROP COLUMN rec_cs_window_ts;
ALTER TABLE results.cd_cohort_relationships DROP COLUMN rec_cs_window_te;
ALTER TABLE results.cd_cohort_relationships DROP COLUMN rec_ce_window_ts;
ALTER TABLE results.cd_cohort_relationships DROP COLUMN rec_ce_window_te;
ALTER TABLE results.cd_cohort_relationships DROP COLUMN rec_c_withi
azimov commented 4 days ago

Apologies for this issue - it should now be reverted