fix reading of csv files for tests

Author: ablack3

R/Incremental.R

@@ -120,7 +120,7 @@ recordTasksDone <-
       recordKeeping <- readr::read_csv(
         file = recordKeepingFile,
         col_types = readr::cols(),
-        guess_max = min(1e7),
+        guess_max = 1e7,
         lazy = FALSE
       )
 

inst/test_cases/runVisitContext/testSubjectCounts/test_getVisitContext_cohort.csv

@@ -1,5 +1,5 @@
-cohort_definition_id,subject_id,cohort_start_date,cohort_end_date
-1,1,1/1/15,1/9/15
-1,2,1/1/15,1/9/15
-2,1,1/10/15,1/20/15
-2,2,1/10/15,1/20/15
+cohort_definition_id,subject_id,cohort_start_date,cohort_end_date
+1,1,2015-01-01,2015-01-09
+1,2,2015-01-01,2015-01-09
+2,1,2015-01-10,2015-01-20
+2,2,2015-01-10,2015-01-20

inst/test_cases/runVisitContext/testSubjectCountsDates/test_getVisitContext_cohort.csv

@@ -1,5 +1,5 @@
-cohort_definition_id,subject_id,cohort_start_date,cohort_end_date
-1,1,1/1/15,1/9/15
-1,2,1/1/15,1/9/15
-2,1,1/10/15,1/20/15
-2,2,1/10/15,1/20/15
+cohort_definition_id,subject_id,cohort_start_date,cohort_end_date
+1,1,2015-01-01,2015-01-09
+1,2,2015-01-01,2015-01-09
+2,1,2015-01-10,2015-01-20
+2,2,2015-01-10,2015-01-20

inst/test_cases/runVisitContext/testSubjectCountsNoVisits/test_getVisitContext_cohort.csv

@@ -1,5 +1,2 @@
-cohort_definition_id,subject_id,cohort_start_date,cohort_end_date
-1,1,1/1/15,1/9/15
-,,,
-,,,
-,,,
+cohort_definition_id,subject_id,cohort_start_date,cohort_end_date
+1,1,2015-01-01,2015-01-09

tests/testthat/helper.R

@@ -173,8 +173,7 @@ createCustomCdm <- function(jsonDataFilePath){
 
 addCohortTable <- function(connection, cohortDataFilePath){
 
-  cohortTableData <- readr::read_csv(cohortDataFilePath, 
-                                     col_types = c("numeric", "numeric", "date", "date"))
+  cohortTableData <- readr::read_csv(cohortDataFilePath, col_types = c("iiDD"))
 
   cohortTableData <- cohortTableData %>% 
     mutate(across(ends_with("DATE"), ~ as.Date(.x, format = "%Y-%m-%d")))

tests/testthat/test-runVisitContext.R

@@ -316,7 +316,7 @@ test_that(paste("test that the subject counts per cohort, visit concept and visi
 
   resultPath <- system.file("test_cases/runVisitContext/testSubjectCounts/expectedResult.csv", package = "CohortDiagnostics")
 
-  resultData <- readr::read_csv(resultPath, col_types = c("numeric", "numeric", "text", "numeric"))
+  resultData <- readr::read_csv(resultPath, col_types = c("ddcd"))
 
   visitContextResult <- visitContextResult[order(visitContextResult$cohortId, visitContextResult$visitConceptId, visitContextResult$visitContext, visitContextResult$subjects), ]
   visitContextResult <- as.data.frame(lapply(visitContextResult, as.character), stringsAsFactors = FALSE)
@@ -436,7 +436,7 @@ test_that(paste("test that to infer subject counts per cohort, visit concept, an
                               package = "CohortDiagnostics", 
                               mustWork = T)
 
-    resultData <- readr::read_csv(resultPath, col_types = c("numeric", "numeric", "text", "numeric"))
+    resultData <- readr::read_csv(resultPath, col_types = c("ddcd"))
 
     visitContextResult <- visitContextResult[order(visitContextResult$cohortId, visitContextResult$visitConceptId, visitContextResult$visitContext, visitContextResult$subjects), ]
     visitContextResult <- as.data.frame(lapply(visitContextResult, as.character), stringsAsFactors = FALSE)
@@ -452,7 +452,9 @@ test_that(paste("test that to infer subject counts per cohort, visit concept, an
 
 test_that(paste("test that no other cohorts than the ones specified in cohortIds are included in the output"), {
 
-  cohortDataFilePath <- system.file("test_cases/runVisitContext/testSubjectCounts/test_getVisitContext_cohort.xlsx",  package = "CohortDiagnostics")
+  cohortDataFilePath <- system.file("test_cases/runVisitContext/testSubjectCounts/test_getVisitContext_cohort.csv",  
+                                    package = "CohortDiagnostics",
+                                    mustWork = TRUE)
 
   patientDataFilePath <- "test_cases/runVisitContext/testSubjectCounts/test_getVisitContext_patientData.json"
 
@@ -479,7 +481,9 @@ test_that(paste("test that no other cohorts than the ones specified in cohortIds
 
 test_that(paste("test that when the subjects in the cohort have no visits an empty data frame is returned"), {
 
-  cohortDataFilePath <- system.file("test_cases/runVisitContext/testSubjectCountsNoVisits/test_getVisitContext_cohort.xlsx",  package = "CohortDiagnostics")
+  cohortDataFilePath <- system.file("test_cases/runVisitContext/testSubjectCountsNoVisits/test_getVisitContext_cohort.csv",  
+                                    package = "CohortDiagnostics",
+                                    mustWork = TRUE)
 
   patientDataFilePath <- "test_cases/runVisitContext/testSubjectCountsNoVisits/test_getVisitContext_patientData.json"
 
@@ -509,7 +513,7 @@ test_that(paste("test that when the subjects in the cohort have no visits an emp
                             package = "CohortDiagnostics",
                             mustWork = TRUE)
 
-  resultData <- readr::read_csv(resultPath, col_types = c("numeric", "numeric", "text", "numeric"))
+  resultData <- readr::read_csv(resultPath, col_types = c("ddcd"))
 
   visitContextResult <- visitContextResult[order(visitContextResult$cohortId, visitContextResult$visitConceptId, visitContextResult$visitContext, visitContextResult$subjects), ]
   visitContextResult <- as.data.frame(lapply(visitContextResult, as.character), stringsAsFactors = FALSE)