Issue with covertToCyclopsData - ORDER By is Ignored in sub queries

[azimov]

In CohortMethod when calling fitOutcomeModel the following warning is thrown:

ORDER BY is ignored in subqueries without LIMIT
ℹ Do you need to move arrange() later in the pipeline or use window_order() instead?
Backtrace:
  1. CohortMethod::runCmAnalyses(...) test-eunomia.R:116:2
  2. ParallelLogger::clusterApply(cluster, modelsToFit, doFitOutcomeModelPlus) /Users/jamie/PycharmProjects/CohortMethod/R/RunAnalyses.R:426:6
  3. base::lapply(x, fun, ...)
  4. CohortMethod:::FUN(X[[i]], ...)
  6. CohortMethod::fitOutcomeModel(...)
  8. Cyclops:::convertToCyclopsData.tbl_dbi(...)
  9. Andromeda::batchApply(covariates, loadCovariates, batchSize = 1e+05)
 11. dbplyr:::sql_render.tbl_lazy(tbl, connection)
 13. dbplyr:::sql_render.op(query$ops, con = con, ..., subquery = subquery)
 15. dbplyr:::sql_render.select_query(qry, con = con, ..., subquery = subquery)
 24. dbplyr:::sql_render.join_query(query$from, con, ..., subquery = TRUE)
 33. dbplyr:::sql_render.tbl_lazy(query$y, con, ..., subquery = TRUE)
 35. dbplyr:::sql_render.op(query$ops, con = con, ..., subquery = subquery)
 37. dbplyr:::sql_render.select_query(qry, con = con, ..., subquery = subquery)
 38. dbplyr:::dbplyr_query_select(...)
 39. dbplyr:::dbplyr_fallback(con, "sql_select", ...)
 41. dbplyr:::sql_select.DBIConnection(con, ...)
 43. dbplyr:::sql_query_select.DBIConnection(...)
 45. dbplyr:::sql_clause_order_by(con, order_by, subquery, limit)
 46. dbplyr:::warn_drop_order_by()

This appears to be a problem with how cyclops is calling Andromeda. Reproducible in the unit tests found here

[msuchard]

@schuemie and I were just discussing this here: OHDSI/Andromeda#25

1. this warning behavior is relatively new (i.e., I have not seen this warning before today, although I have not looked in several months)
2. am not sure if this really is an issue or not
3. i could definitely use some help in tracking down the issue

[schuemie]

Found it. Under specific conditions outcomes is being sorted here, and then joined to covariates here, at which time the sorting is lost (in the join, not in the outcomes object). This has no effect on the final result, but the warning is annoying. It can be fixed by joining before applying the sort on outcomes.

[msuchard]

Great work, @schuemie !