From ceebb3e1a0cbfaa34a6412c3742abc7f8b3aa3dd Mon Sep 17 00:00:00 2001
From: Katy Sadowski <katy.h.sadowski@gmail.com>
Date: Mon, 16 Oct 2023 12:19:42 -0400
Subject: [PATCH 1/2] add readr local edition downgrade

---
 R/convertResultsCase.R | 3 +++
 R/executeDqChecks.R    | 3 +++
 R/listChecks.R         | 4 ++++
 man/executeDqChecks.Rd | 2 +-
 4 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/R/convertResultsCase.R b/R/convertResultsCase.R
index 0668b211..92c77f77 100644
--- a/R/convertResultsCase.R
+++ b/R/convertResultsCase.R
@@ -46,6 +46,9 @@ 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
index 500de89c..aa38ee5e 100644
--- a/R/executeDqChecks.R
+++ b/R/executeDqChecks.R
@@ -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
index ddeccbb4..db7ff3b3 100644
--- a/R/listChecks.R
+++ b/R/listChecks.R
@@ -28,6 +28,10 @@
 #'
 #' @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
index 1ae7d2e2..0b7b5f7f 100644
--- a/man/executeDqChecks.Rd
+++ b/man/executeDqChecks.Rd
@@ -92,5 +92,5 @@ with the fields cohort_definition_id and subject_id.}
 If sqlOnly = FALSE, a list object of results
 }
 \description{
-This function will connect to the database, generate the sql scripts, and run the data quality checks against the database.
+This function will connect to the database, generate the sql scripts, and run the data quality checks against the database. By default, results will be written to a json file as well as a database table.
 }

From ca1a9419a48b060a8531c0f6b071dee999dbc031 Mon Sep 17 00:00:00 2001
From: Katy Sadowski <katy.h.sadowski@gmail.com>
Date: Mon, 16 Oct 2023 12:35:04 -0400
Subject: [PATCH 2/2] fix naming conflict, add imports

---
 NAMESPACE                             | 1 +
 R/convertResultsCase.R                | 1 +
 R/executeDqChecks.R                   | 2 +-
 R/listChecks.R                        | 2 +-
 tests/testthat/test-executeDqChecks.R | 2 +-
 5 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 69aad71c..690105a7 100644
--- 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
index 92c77f77..73aa5954 100644
--- 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
 
diff --git a/R/executeDqChecks.R b/R/executeDqChecks.R
index aa38ee5e..9cfd44fc 100644
--- 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
diff --git a/R/listChecks.R b/R/listChecks.R
index db7ff3b3..29ca602f 100644
--- a/R/listChecks.R
+++ b/R/listChecks.R
@@ -24,7 +24,7 @@
 #' @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") {
diff --git a/tests/testthat/test-executeDqChecks.R b/tests/testthat/test-executeDqChecks.R
index e7cb2abf..01cb11b3 100644
--- 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_")