Script stops unexpectedtly with empty table df.conditions

[mw-uke]

Hi all, the script stops unexpectedly after retrieving Medication resources with the following log output:

projectathon6-miracum1_1  | Warning message:
projectathon6-miracum1_1  | Problem while computing `rank_indicator = min(rank)`.
projectathon6-miracum1_1  | ℹ no non-missing arguments, returning NA
projectathon6-miracum1_1  | Error in `summarise()`:
projectathon6-miracum1_1  | ! Problem while computing `percent_encounters = paste0(...)`.
projectathon6-miracum1_1  | ℹ The error occurred in group 1: procedures = "Admission to stroke unit".
projectathon6-miracum1_1  | Caused by error in `unique()`:
projectathon6-miracum1_1  | ! object 'df.cohort.trunc' not found
projectathon6-miracum1_1  | Backtrace:
projectathon6-miracum1_1  |      ▆
projectathon6-miracum1_1  |   1. ├─df.procedure %>% group_by(procedures = features) %>% ...
projectathon6-miracum1_1  |   2. ├─dplyr::summarise(...)
projectathon6-miracum1_1  |   3. ├─dplyr:::summarise.grouped_df(...)
projectathon6-miracum1_1  |   4. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), caller_env = caller_env())
projectathon6-miracum1_1  |   5. │   ├─base::withCallingHandlers(...)
projectathon6-miracum1_1  |   6. │   └─dplyr:::map(quosures, summarise_eval_one, mask = mask)
projectathon6-miracum1_1  |   7. │     └─base::lapply(.x, .f, ...)
projectathon6-miracum1_1  |   8. │       └─dplyr FUN(X[[i]], ...)
projectathon6-miracum1_1  |   9. │         └─mask$eval_all_summarise(quo)
projectathon6-miracum1_1  |  10. ├─base::paste0(...)
projectathon6-miracum1_1  |  11. ├─base::unique(df.cohort.trunc$encounter_id)
projectathon6-miracum1_1  |  12. └─base::.handleSimpleError(...)
projectathon6-miracum1_1  |  13.   └─dplyr h(simpleError(msg, call))
projectathon6-miracum1_1  |  14.     └─rlang::abort(bullets, call = error_call, parent = skip_internal_condition(e))
projectathon6-miracum1_1  | Execution halted
projectathon6_projectathon6-miracum1_1 exited with code 1

Using nandhinis08/projectathon6-miracum1 from dockerhub with docker-compose.

After some initial debugging I can say that:

• df.encounters contains (seemingly) valid entires
• df.conditions is empty - this might be the reason for stopping?
• df.cohort is empty

Any ideas?

[NandhiniS08]

May I ask if you have condition resources in your FHIR server? Do you have the possibility of running the code in Rstudio?

[mw-uke]

Hi @NandhiniS08, yes we do have Condition resources, but there was indeed an issue with an incorrect code system in our resources which led to an empty df.conditions table, which then crashed the script. This is now resolved and the script runs fine.

Thanks for looking into this and sorry for any inconvenience.

[NandhiniS08]

Thanks for the update! No problem. I am glad it's running fine.