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ohdsi-studies / PioneerWatchfulWaiting

This study is part of the joint PIONEER - EHDEN - OHDSI studyathon in March 2021, and aims to advance understanding of clinical management and outcomes of watchful waiting in prostate cancer.
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changed cohorts #63

Closed denyskaduk closed 3 years ago

keesvanbochove commented 3 years ago

Hi @denyskaduk I see you propose to merge an older commit with manual changes to the SQL definitions of some target cohorts into master, is this to re-apply those changes? It could work but in that case could you resolve the merge conflicts?

denyskaduk commented 3 years ago

HI, I'm on testing them now, how finish, will inform

denyskaduk commented 3 years ago

cohorts creation checked and fixed, was tested on synthetic data

bdemeulder commented 3 years ago

@keesvanbochove, can you review in lieu of Maxim?

keesvanbochove commented 3 years ago

@denyskaduk after setting episodetable to FALSE, it creates the first few cohorts but halts on cohort 105.sql: 

5/70: Instantiation cohort [PIONEER T3.1] PCa high/intermediate risk conservative management  (105.sql)
  |===============================                                       |  44%Error: Error executing SQL:
org.postgresql.util.PSQLException: ERROR: syntax error at or near "======="
  Position: 3203

Looks like a remnant of a merge conflict that wasn't fully solved, could you check this?

keesvanbochove commented 3 years ago

OK, I've tested it against a Synthea database and both cohort diagnostics generation and runStudy work now, although I can't test everything because I'm not getting any target cohort counts in my synthetic data set. Also I will look into bumping CohortDiagnostics to v2.2 because I'm seeing a few issues there, but for now I think we should merge this into master.