(Hopefully temporary) workaround for tidyverse/vroom#519

OHDSI · Oct 31, 2023 · 94ac999 · 94ac999
1 parent 8e66100
commit 94ac999
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Showing 4 changed files with 6 additions and 8 deletions.
diff --git a/R/Export.R b/R/Export.R
@@ -134,6 +134,8 @@ writeToCsv <- function(data, fileName, append = FALSE) {
     data <- createEmptyResult(tableName)
   }
   colnames(data) <- SqlRender::camelCaseToSnakeCase(colnames(data))
+  # Workaround for issue https://github.com/tidyverse/vroom/issues/519:
+  readr::local_edition(1)
   readr::write_csv(x = data, file = fileName, append = append)
 }
 

diff --git a/R/ResultsDataModel.R b/R/ResultsDataModel.R
@@ -23,6 +23,8 @@
 #' @export
 getResultsDataModelSpecifications <- function() {
   pathToCsv <- system.file("csv", "resultsDataModelSpecification.csv", package = utils::packageName())
+  # Workaround for issue https://github.com/tidyverse/vroom/issues/519:
+  readr::local_edition(1)
   resultsDataModelSpecifications <- readr::read_csv(file = pathToCsv, col_types = readr::cols())
   colnames(resultsDataModelSpecifications) <- SqlRender::snakeCaseToCamelCase(colnames(resultsDataModelSpecifications))
   return(resultsDataModelSpecifications)

diff --git a/extras/UploadResultsToSqlite.R b/extras/UploadResultsToSqlite.R
@@ -19,14 +19,6 @@ file.copy(
   to = file.path(outputFolder, "export")
 )
 
-# csv <- readr::read_csv(system.file("csv", "resultsDataModelSpecification.csv", package = "SelfControlledCaseSeries"))
-# csv$empty_is_na <- FALSE
-# csv$is_required[csv$table_name == "sccs_covariate" & csv$column_name == "covariate_analysis_id"] <- "No"
-# csv$primary_key[csv$table_name == "sccs_age_spanning" & csv$column_name == "age_month"] <- "Yes"
-# csv$primary_key[csv$table_name == "sccs_calendar_time_spanning" & csv$column_name == "year"] <- "Yes"
-# csv$primary_key[csv$table_name == "sccs_calendar_time_spanning" & csv$column_name == "month"] <- "Yes"
-# readr::write_csv(csv, file.path(outputFolder, "export", "resultsDataModelSpecification.csv"))
-
 createResultsDataModelTables(
   connectionDetails = connectionDetails,
   schema = "main",

diff --git a/tests/testthat/test-eunomia.R b/tests/testthat/test-eunomia.R
@@ -168,6 +168,8 @@ test_that("Running multiple analyses against Eunomia", {
   # Test export to CSV:
   exportToCsv(outputFolder)
 
+  # Workaround for issue https://github.com/tidyverse/vroom/issues/519:
+  readr::local_edition(1)
   diagnosticsSummary <- readr::read_csv(file.path(outputFolder, "export", "sccs_diagnostics_summary.csv"), show_col_types = FALSE)
   expect_true(all(diagnosticsSummary$ease_diagnostic == "NOT EVALUATED"))