Merge pull request #495 from katy-sadowski/katy__vroom_fix

Add readr local edition downgrade
OHDSI · Oct 18, 2023 · cd5bd33 · cd5bd33
2 parents b1eb194 + ca1a941
commit cd5bd33
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Showing 6 changed files with 16 additions and 4 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -18,6 +18,7 @@ importFrom(jsonlite,fromJSON)
 importFrom(jsonlite,parse_json)
 importFrom(jsonlite,toJSON)
 importFrom(magrittr,"%>%")
+importFrom(readr,local_edition)
 importFrom(readr,read_csv)
 importFrom(rlang,.data)
 importFrom(stats,na.omit)

diff --git a/R/convertResultsCase.R b/R/convertResultsCase.R
@@ -30,6 +30,7 @@
 #' @importFrom SqlRender snakeCaseToCamelCase camelCaseToSnakeCase
 #' @importFrom dplyr rename_with
 #' @importFrom tools file_path_sans_ext
+#' @importFrom readr local_edition
 #'
 #' @export
 
@@ -46,6 +47,9 @@ convertJsonResultsFileCase <- function(
   if (writeToFile && is.na(outputFolder)) {
     stop("You must specify an output folder if writing to file.")
   }
+
+  # temporary patch to work around vroom 1.6.4 bug
+  readr::local_edition(1)
 
   results <- jsonlite::fromJSON(jsonFilePath)
 

diff --git a/R/executeDqChecks.R b/R/executeDqChecks.R
@@ -54,7 +54,7 @@
 #' @importFrom utils packageVersion write.table
 #' @importFrom rlang .data
 #' @importFrom tidyselect all_of
-#' @importFrom readr read_csv
+#' @importFrom readr read_csv local_edition
 #' @importFrom dplyr mutate case_when
 #'
 #' @export
@@ -118,6 +118,9 @@ executeDqChecks <- function(connectionDetails,
       warning(sprintf("Missing check names to calculate the 'Not Applicable' status: %s", missingNACheckNames))
     }
   }
+
+  # temporary patch to work around vroom 1.6.4 bug
+  readr::local_edition(1)
 
   # capture metadata -----------------------------------------------------------------------
   if (!sqlOnly) {

diff --git a/R/listChecks.R b/R/listChecks.R
@@ -24,10 +24,14 @@
 #' @param fieldCheckThresholdLoc    The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied.
 #' @param conceptCheckThresholdLoc  The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied.
 #'
-#' @importFrom readr read_csv
+#' @importFrom readr read_csv local_edition
 #'
 #' @export
 listDqChecks <- function(cdmVersion = "5.3", tableCheckThresholdLoc = "default", fieldCheckThresholdLoc = "default", conceptCheckThresholdLoc = "default") {
+
+  # temporary patch to work around vroom 1.6.4 bug
+  readr::local_edition(1)
+
   dqChecks <- {}
   dqChecks$checkDescriptions <-
     read_csv(system.file(

diff --git a/man/executeDqChecks.Rd b/man/executeDqChecks.Rd
diff --git a/tests/testthat/test-executeDqChecks.R b/tests/testthat/test-executeDqChecks.R
@@ -1,5 +1,5 @@
 library(testthat)
-local_edition(3)
+testthat::local_edition(3)
 
 test_that("Execute a single DQ check on Synthea/Eunomia", {
   outputFolder <- tempfile("dqd_")