Column `X_CALENDAR_MONTH` doesn't exist

[keesvanbochove]

When running the package on Truven claims dataset, results generation works fine but then when creating the Word document the script breaks on a column which it expects but isn't there (see https://github.com/EHDEN/CdmInspection/blob/712bc3fa97d36c66121a8ae8776c594be4100043/R/Helper.R#L128). What could cause this? Can we skip generation of these plots?

Error: Can't rename columns that don't exist. x Column X_CALENDAR_MONTH doesn't exist. Traceback:

1. generateResultsDocument(obj, outputFolder, authors = authors, . databaseDescription = databaseDescription, databaseName = databaseName, . databaseId = databaseId, smallCellCount = smallCellCount)
2. recordsCountPlot(as.data.frame(results$dataTablesResults$totalRecords$result))
3. results %>% dplyr::rename(Date = X_CALENDAR_MONTH, Domain = SERIES_NAME, . Count = Y_RECORD_COUNT) %>% dplyr::mutate(Date = lubridate::parse_date_time(Date, . "ym"))
4. dplyr::mutate(., Date = lubridate::parse_date_time(Date, "ym"))
5. dplyr::rename(., Date = X_CALENDAR_MONTH, Domain = SERIES_NAME, . Count = Y_RECORD_COUNT)
6. rename.data.frame(., Date = X_CALENDAR_MONTH, Domain = SERIES_NAME, . Count = Y_RECORD_COUNT)
7. tidyselect::eval_rename(expr(c(...)), .data)
8. rename_impl(data, names(data), as_quosure(expr, env), strict = strict, . name_spec = name_spec)
9. eval_select_impl(x, names, { . { . sel . } . }, strict = strict, name_spec = name_spec, type = "rename")
10. with_subscript_errors(vars_select_eval(vars, expr, strict, data = x, . name_spec = name_spec, uniquely_named = uniquely_named, allow_rename = allow_rename, . type = type), type = type)
11. tryCatch(instrument_base_errors(expr), vctrs_error_subscript = function(cnd) { . cnd$subscript_action <- subscript_action(type) . cnd$subscript_elt <- "column" . cnd_signal(cnd) . })
12. tryCatchList(expr, classes, parentenv, handlers)
13. tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. value[3L]
15. cnd_signal(cnd)
16. rlang:::signal_abort(x)

[keesvanbochove]

Workaround is to disable the plots: in between calling cdmInspection and generateResultsDocument, run: results$dataTablesResults <- NULL With thanks to @MaximMoinat.

[PRijnbeek]

Do not really understand what the problem is, have not seen it before on the databases. Was Achilles run on the database prior to running cdmInspection and are the results in the schema you defined?

[MaximMoinat]

That is very likely the issue. We might want to detect this and give a warning that Achilles has not been run yet (or make this in another way very explicit).

On Thu, 4 Mar 2021, 15:09 Peter Rijnbeek, notifications@github.com wrote:

Do not really understand what the problem is, have not seen it before on the databases. Was Achilles run on the database prior to running cdmInspection and are the results in the schema you defined?

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[PRijnbeek]

Yes agreed, it is in the Readme but we can add a message in the package