e

R/CreateCohortExplorerApp.R

@@ -57,7 +57,7 @@
 #'                                    replace the personId in the source with a randomly assigned newId.
 #' @param featureCohortDatabaseSchema The CohortDatabaseSchema where the feature cohort table exits.
 #' @param featureCohortTable          The Cohort table where feature cohorts are instantiated.
-#' @param featureCohortDefinitionSet  The CohortDefinitionSet object corresponding to the cohorts to 
+#' @param featureCohortDefinitionSet  The CohortDefinitionSet object corresponding to the cohorts to
 #'                                    be used as features.
 #' @returns                           Returns invisibly the full path of the export folder where the
 #'                                    files were created. In this path are the files that are part of the 'shiny'
@@ -202,7 +202,7 @@ createCohortExplorerApp <- function(connectionDetails = NULL,
     access = "x",
     add = errorMessage
   )
-  
+
   useCohortDomain <- FALSE
   if (any(
     !is.null(featureCohortDefinitionSet),
@@ -731,7 +731,7 @@ createCohortExplorerApp <- function(connectionDetails = NULL,
   ) %>%
     dplyr::tibble() %>%
     dplyr::mutate(endDate = .data$startDate)
-  
+
   featureCohortData <- NULL
   if (useCohortDomain) {
     writeLines("Getting feature cohort table.")
@@ -1174,10 +1174,12 @@ createCohortExplorerApp <- function(connectionDetails = NULL,
     data = measurement,
     useNewId = assignNewId
   )
-  
+
   if (!is.null(featureCohortData)) {
-    featureCohortData <- replaceId(data = featureCohortData,
-                                   useNewId = assignNewId)
+    featureCohortData <- replaceId(
+      data = featureCohortData,
+      useNewId = assignNewId
+    )
   }
 
   results <- list(

R/Helper.R

@@ -29,10 +29,10 @@ replaceId <- function(data, useNewId = TRUE) {
 addDays <- function(x, n) {
   # Ensure that x is of class Date
   xAsDate <- as.Date(x)
-  
+
   # Add n days to xAsDate
   newDate <- xAsDate + as.integer(n)
-  
+
   return(newDate)
 }
 

tests/testthat/test-createCohortExplorerApp.R

@@ -332,13 +332,13 @@ test_that("do Not Export CohortData", {
 
 test_that("use cohort features", {
   skip_if(skipCdmTests, "CDM settings not configured")
-  
+
   library(dplyr)
-  
+
   connection <-
     DatabaseConnector::connect(connectionDetails = connectionDetails)
   on.exit(DatabaseConnector::disconnect(connection))
-  
+
   # create a cohort with 1000 persons
   createCohortTableSql <- "
     DROP TABLE IF EXISTS @cohort_database_schema.@cohort_table;
@@ -374,7 +374,7 @@ test_that("use cohort features", {
             2 cohort_definition_id,
             cohort_start_date,
             cohort_end_date
-    FROM @cohort_database_schema.@cohort_table 
+    FROM @cohort_database_schema.@cohort_table
     WHERE cohort_definition_id = 1;
 
     INSERT INTO @cohort_database_schema.@cohort_table
@@ -384,10 +384,12 @@ test_that("use cohort features", {
             cohort_end_date
     FROM @cohort_database_schema.@cohort_table
     WHERE cohort_definition_id = 1;"
-
-  featureCohortDefinitionSet <- dplyr::tibble(cohortId = 2,
-                                              cohortName = "same cohort")
-
+
+  featureCohortDefinitionSet <- dplyr::tibble(
+    cohortId = 2,
+    cohortName = "same cohort"
+  )
+
   DatabaseConnector::renderTranslateExecuteSql(
     connection = connection,
     sql = createCohortTableSql,
@@ -396,12 +398,12 @@ test_that("use cohort features", {
     reportOverallTime = FALSE,
     cohort_database_schema = cohortDatabaseSchema,
     cdm_database_schema = cdmDatabaseSchema,
-    cohort_table = cohortTable, 
+    cohort_table = cohortTable,
     tempEmulationSchema = tempEmulationSchema
   )
-  
+
   outputDir <- tempfile()
-  
+
   outputPath <- createCohortExplorerApp(
     connection = connection,
     cdmDatabaseSchema = cdmDatabaseSchema,
@@ -412,18 +414,18 @@ test_that("use cohort features", {
     exportFolder = outputDir,
     featureCohortDatabaseSchema = cohortDatabaseSchema,
     featureCohortDefinitionSet = featureCohortDefinitionSet,
-    featureCohortTable = cohortTable, 
+    featureCohortTable = cohortTable,
     cohortDefinitionId = 1
   )
-  
+
   testthat::expect_true(file.exists(
     file.path(
       outputPath,
       "data",
       "CohortExplorer_1_databaseData.rds"
     )
   ))
-  
+
   testthat::expect_error(
     createCohortExplorerApp(
       connection = connection,