Fixes #1261 throw an error if data is not utf-8 encoded (#1265)

* Fixes #1261 throw an error if data is not utf-8 encoded * Test dictionaries had non utf-8 characters
Open-Systems-Pharmacology · Sep 6, 2024 · f736335 · f736335
1 parent 252a166
commit f736335
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Showing 8 changed files with 343 additions and 6 deletions.
diff --git a/R/utilities-observed-data.R b/R/utilities-observed-data.R
@@ -66,6 +66,7 @@ readObservedDataFile <- function(fileName,
                                  header = TRUE,
                                  encoding = "UTF-8") {
   validateFileExists(fileName)
+  validateIsFileUTF8(fileName)
   # Get function with the most appropriate reading defaults
   readObservedData <- getReaderFunction(fileName)
   observedData <- readObservedData(

diff --git a/tests/data/input-data/non-utf8.txt b/tests/data/input-data/non-utf8.txt
diff --git a/tests/data/input-data/tpDictionary-ill-defined-unit.csv b/tests/data/input-data/tpDictionary-ill-defined-unit.csv
@@ -7,5 +7,5 @@ tad,timeprofile,TAD,h,,,
 age,covariate,AGE,year(s),Age,Organism|Age,
 wght,covariate,WGHT,kg,Body weight,Organism|Weight,
 hght,covariate,HGHT,cm,Height,Organism|Height,
-bmi,covariate,BMI,kg/m�,BMI,Organism|BMI,
+bmi,covariate,BMI,kg/m²,BMI,Organism|BMI,
 gender,covariate,SEX,,SEX,Gender,Make sure 1=male  2= female
diff --git a/tests/data/input-data/tpDictionary-ill-defined-variable.csv b/tests/data/input-data/tpDictionary-ill-defined-variable.csv
@@ -7,5 +7,5 @@ tad,timeprofile,TAD,h,,,
 age,covariate,AGE,year(s),Age,Organism|Age,
 wght,covariate,WGHT,kg,Body weight,Organism|Weight,
 hght,covariate,HGHT,cm,Height,Organism|Height,
-bmi,covariate,BMI,kg/m�,BMI,Organism|BMI,
+bmi,covariate,BMI,kg/m²,BMI,Organism|BMI,
 gender,covariate,SEX,,SEX,Gender,Make sure 1=male  2= female
diff --git a/tests/data/input-data/tpDictionary-lloq.csv b/tests/data/input-data/tpDictionary-lloq.csv
@@ -8,5 +8,5 @@ lloq,timeprofile,LOQ,µmol/l,,,
 age,covariate,AGE,year(s),Age,Organism|Age,
 wght,covariate,WGHT,kg,Body weight,Organism|Weight,
 hght,covariate,HGHT,cm,Height,Organism|Height,
-bmi,covariate,BMI,kg/m�,BMI,Organism|BMI,
+bmi,covariate,BMI,kg/m²,BMI,Organism|BMI,
 gender,covariate,SEX,,SEX,Gender,Make sure 1=male  2= female
diff --git a/tests/data/input-data/tpDictionary-unit-in-obs.csv b/tests/data/input-data/tpDictionary-unit-in-obs.csv
@@ -8,5 +8,5 @@ tad,timeprofile,TAD,h,,,
 age,covariate,AGE,year(s),Age,Organism|Age,
 wght,covariate,WGHT,kg,Body weight,Organism|Weight,
 hght,covariate,HGHT,cm,Height,Organism|Height,
-bmi,covariate,BMI,kg/m�,BMI,Organism|BMI,
+bmi,covariate,BMI,kg/m²,BMI,Organism|BMI,
 gender,covariate,SEX,,SEX,Gender,Make sure 1=male  2= female
diff --git a/tests/data/input-data/tpDictionary.csv b/tests/data/input-data/tpDictionary.csv
@@ -7,5 +7,5 @@ tad,timeprofile,TAD,h,,,
 age,covariate,AGE,year(s),Age,Organism|Age,
 wght,covariate,WGHT,kg,Body weight,Organism|Weight,
 hght,covariate,HGHT,cm,Height,Organism|Height,
-bmi,covariate,BMI,kg/m�,BMI,Organism|BMI,
+bmi,covariate,BMI,kg/m²,BMI,Organism|BMI,
 gender,covariate,SEX,,SEX,Gender,Make sure 1=male  2= female
diff --git a/tests/testthat/test-observed-data.R b/tests/testthat/test-observed-data.R
@@ -49,10 +49,16 @@ test_that("readObservedDataFile can correctly guess separator and read csv and t
   expect_equal(testDataFrame, txtData, tolerance = comparisonTolerance())
 })
 
-test_that("readObservedDataFile: unexistant file throw error", {
+test_that("readObservedDataFile: throws an error for unexistant files", {
   expect_error(readObservedDataFile("testFile10.csv"))
 })
 
+test_that("readObservedDataFile throws an error for non UTF-8 files", {
+  expect_error(
+    readObservedDataFile(getTestDataFilePath("input-data/non-utf8.txt"))
+    )
+})
+
 test_that("readObservedDataFile throw an error if columns are inconsistent", {
   expect_error(
     readObservedDataFile(getTestDataFilePath("input-data/error-data.csv"))