tests/testthat/test-createRDBESDataObject.R
In ices-tools-dev/icesRDBES: Functions for the ICES Regional Database and Estimation System (RDBES)
capture.output({ ## suppresses printing of console output when running test()
# common parameters
# H1 directory
dirH1 <- "./h1_v_20250211/"
# H5 directory
dirH5 <- "./h5_v_20250211/"
# H7 directory
dirH7 <- "./h7_v_1_19_26/"
# H1 object for comparison
expObjH1 <- H1Example
# Test general behavior --------------------------------------------------
test_that("createRDBESDataObject will give a warning if given a dir with no relevant files in it", {
myPath <- "."
expect_warning(createRDBESDataObject(input = myPath),"No relevant files found in given directory - an empty object will be created")
})
test_that("Expect warning when the input is not csv, list of dfs, zip files, NULL - Test Integer input", {
myPath <- as.integer(1)
expect_error(createRDBESDataObject(myPath), "Input type not recognised. Should be a RDBES zip file, folder of csv files, or list of data frames.")
})
test_that("Expect warning when the input is not csv, list of dfs, zip files, NULL - Test dataframe input", {
myPath <- as.data.frame(1)
expect_error(createRDBESDataObject(myPath), "Input type not recognised. Should be a RDBES zip file, folder of csv files, or list of data frames.")
})
test_that("createRDBESDataObject will throw an error when given multiple inputs", {
zipFiles <- c(
"H1_Example.zip"
)
H1 <- paste0(dirH1, zipFiles)
df <- as.data.frame(1)
expect_error(createRDBESDataObject(input = c(H1, df, dirH1)), "Input type not recognised. Should be a RDBES zip file, folder of csv files, or list of data frames.")
})
# Test ZIP inputs ---------------------------------------------------------
test_that("importing foldered zipped H1 example data works", {
zipFiles <- c(
"H1_Example_fd.zip"
)
genObj <- createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE)
expect_equal(genObj, expObjH1)
})
test_that("importing foldered zipped H1 and H2 gives an error", {
zipFiles <- c(
"H1_H2_Example_fd.zip"
)
genObj <- expect_error(
createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE),
"The zip file contains multiple hierarchies.\nTo import a selected hierarchy, please provide the hierarchy as an argument e.g like:\nHierachy = 1"
)
})
test_that("importing foldered zipped H1 and H2 example data works when hierarchy is specified", {
zipFiles <- c(
"H1_H2_Example_fd.zip"
)
genObj <- createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE,
Hierarchy = 1)
expect_equal(genObj, expObjH1)
})
test_that("importing foldered zipped H1 and H2 example does not work when hierarchy is misspecified", {
zipFiles <- c(
"H1_H2_Example_fd.zip"
)
genObj <- expect_error(
createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE,
Hierarchy = "H1"),
"The zip file does not contain the hierarchy specified. The options are: 1, 2\nPlease provide a valid hierarchy as an argument. e.g like:\nHierachy = 1"
)
})
test_that("importing zipped H1 example data works", {
zipFiles <- c(
"H1_Example.zip"
)
genObj <- createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE)
expect_equal(genObj, expObjH1)
})
test_that("importing some data that is not zipped with some data that are zipped H1 example data should not work", {
zipFiles <- c(
"H1_Example.zip",
"HSL_Example.zip",
"VesselDetails.csv"
)
genObj <- expect_error(
createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE),
"You cannot import a mix of 'csv' and 'zip' inputs. To import multiple tables unzip all files and import as a folder of 'csv' files."
)
})
test_that("importing subset H1 example data works", {
zipFiles <- c(
"HSL_Example.zip",
"HVD_Example.zip"
)
genObj <- createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE)
expect_equal(genObj$VD, expObjH1$VD)
expect_equal(genObj$SS, NULL)
expect_equal(genObj$SL, expObjH1$SL)
})
test_that("Overwriting a table from a zip file produces a warning", {
zipFiles <- c(
"H1_Example.zip",
"HVD_Example.zip")
expect_warning(
createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = FALSE),
"Duplicate unzipped files detected:\n")
})
test_that("The order of importing should not matter", {
zipFiles1 <- c(
"H1_Example.zip",
"HVD_Example.zip")
genObj1 <- suppressWarnings(
createRDBESDataObject(paste0(dirH1, zipFiles1),
castToCorrectDataTypes = TRUE))
zipFiles2 <- c("HVD_Example.zip",
"H1_Example.zip")
genObj2 <- suppressWarnings(
createRDBESDataObject(paste0(dirH1, zipFiles2),
castToCorrectDataTypes = TRUE))
expect_equal(genObj1$VD, genObj2$VD)
expect_equal(genObj1$SS, genObj2$SS)
expect_equal(genObj1$SL, genObj2$SL)
expect_equal(genObj1$FT, genObj2$FT)
expect_equal(genObj1, genObj2)
})
test_that("createRDBESDataObject creates an object with the correct data types", {
zipFiles <- c(
"H1_Example.zip",
"HVD_Example.zip")
genObj <- suppressWarnings(createRDBESDataObject(input = paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE))
myDiffs <- validateRDBESDataObjectDataTypes(genObj)
numberOfDifferences <- nrow(myDiffs)
expect_equal(numberOfDifferences,0)
})
# Test CSV inputs ---------------------------------------------------------
test_that("createRDBESDataObject can create an object from a H1 data extract
without errors or warnings", {
csvFilesH1 <- dirH1
expect_warning(createRDBESDataObject(input = csvFilesH1), NA)
expect_error(createRDBESDataObject(input = csvFilesH1), NA)
})
test_that("createRDBESDataObject can create an object from a H1 data extract
without errors or warnings (when castToCorrectDataTypes = FALSE)", {
csvFilesH1 <- dirH1
expect_warning(
createRDBESDataObject(input = csvFilesH1,
castToCorrectDataTypes = FALSE), NA)
expect_error(
createRDBESDataObject(input = csvFilesH1,
castToCorrectDataTypes = FALSE), NA)
})
test_that("createRDBESDataObject can create an object from a H1 data extract
with the right number of rows", {
csvFilesH1 <- dirH1
myH1 <- createRDBESDataObject(input = csvFilesH1)
# Get the default file names
fileNames <- RDBEScore::DefaultFileNames
# Remove any unnecessary files
fileNames[names(fileNames) %in% c("TE","LO","OS","LE")] <- NULL
# Append the right path
fileNames <-lapply(fileNames, function(x){paste(csvFilesH1,x,".csv",sep="")})
# Read the number of rows in each file
fileNumberOfRows <- lapply(fileNames, function(x){length(readLines(x))-1})
# For each file
for(x in names(fileNumberOfRows)){
# check if the value of nrow is equal to the length of readlines()-1
expect_true(nrow(myH1[[x]]) == fileNumberOfRows[x])
}
})
test_that("createRDBESDataObject can create an object from an H5 data extract
without errors or warnings", {
csvFilesH5 <- dirH5
expect_warning(createRDBESDataObject(input = csvFilesH5), NA)
expect_error(createRDBESDataObject(input = csvFilesH5), NA)
})
test_that("createRDBESDataObject can create an object from an H5 data extract
without errors or warnings (when castToCorrectDataTypes = FALSE)", {
csvFilesH5 <- dirH5
expect_warning(
createRDBESDataObject(input = csvFilesH5,
castToCorrectDataTypes = FALSE), NA)
expect_error(
createRDBESDataObject(input = csvFilesH5,
castToCorrectDataTypes = FALSE), NA)
})
test_that("createRDBESDataObject can create an object from a H5 data extract
with the right number of rows", {
csvFilesH5 <- dirH5
myH5 <- createRDBESDataObject(input = csvFilesH5)
# Get the default file names
fileNames <- RDBEScore::DefaultFileNames
# Remove any unnecessary files
fileNames[names(fileNames) %in% c("TE","LO","VS","FO")] <- NULL
# Append the right path
fileNames <-lapply(fileNames, function(x){paste(csvFilesH5,x,".csv",sep="")})
# Read the number of rows in each file
fileNumberOfRows <- lapply(fileNames, function(x){length(readLines(x))-1})
# For each file
for(x in names(fileNumberOfRows)){
# check if the value of nrow is equal to the length of readlines()-1
expect_true(nrow(myH5[[x]]) == fileNumberOfRows[x])
}
})
test_that("createRDBESDataObject can create an object from an H1 data extract by specifying file names without errors or warnings", {
csvFilesH1 <- dirH1
myFileNames <- list("DE"="DE.csv","SD"="SD.csv")
myObject <- expect_warning(createRDBESDataObject(input = csvFilesH1, listOfFileNames = myFileNames), NA)
myObject <- expect_error(createRDBESDataObject(input = csvFilesH1, listOfFileNames = myFileNames), NA)
})
test_that("createRDBESDataObject returns warning when input = NULL & the listofFileNames is not", {
csvFilesH1 <- NULL
myFileNames <- list("DE"="DE.csv","SD"="SD.csv")
expect_warning(createRDBESDataObject(input = csvFilesH1, listOfFileNames = myFileNames), NA)
})
test_that("createRDBESDataObject creates an object with the correct data types", {
csvFilesH1 <- dirH1
myRDBESDataObject <- createRDBESDataObject(input = csvFilesH1,
castToCorrectDataTypes = TRUE)
myDiffs <- validateRDBESDataObjectDataTypes(myRDBESDataObject)
numberOfDifferences <- nrow(myDiffs)
expect_equal(numberOfDifferences,0)
})
test_that("createRDBESDataObject creates an H1 object with keys on the data tables", {
csvFilesH1 <- dirH1
myRDBESDataObject <- createRDBESDataObject(input = csvFilesH1)
# Not all of the RDBES table types are in the sample data
expectedNumberOfTablesWithKeys <- 14
actualNumberOfTablesWithKeys <- 0
for(aTable in names(myRDBESDataObject)){
if ('data.table' %in% class(myRDBESDataObject[[aTable]])){
if (!is.null(data.table::key(myRDBESDataObject[[aTable]]))){
actualNumberOfTablesWithKeys <- actualNumberOfTablesWithKeys + 1
}
}
}
expect_equal(expectedNumberOfTablesWithKeys,actualNumberOfTablesWithKeys)
})
test_that("createRDBESDataObject creates an H5 object with keys on the data tables", {
csvFilesH5 <- dirH5
myRDBESDataObject <- createRDBESDataObject(input = csvFilesH5)
# Not all of the RDBES table types are in the sample data
expectedNumberOfTablesWithKeys <- 14
actualNumberOfTablesWithKeys <- 0
for(aTable in names(myRDBESDataObject)){
if ('data.table' %in% class(myRDBESDataObject[[aTable]])){
if (!is.null(data.table::key(myRDBESDataObject[[aTable]]))){
actualNumberOfTablesWithKeys <- actualNumberOfTablesWithKeys + 1
}
}
}
expect_equal(expectedNumberOfTablesWithKeys,actualNumberOfTablesWithKeys)
})
test_that("createRDBESDataObject creates an H7 object with keys on the data tables", {
csvFilesH7 <- dirH7
myRDBESDataObject <- createRDBESDataObject(input = csvFilesH7)
# Not all of the RDBES table types are in the sample data
expectedNumberOfTablesWithKeys <- 13
actualNumberOfTablesWithKeys <- 0
for(aTable in names(myRDBESDataObject)){
if ('data.table' %in% class(myRDBESDataObject[[aTable]])){
if (!is.null(data.table::key(myRDBESDataObject[[aTable]]))){
actualNumberOfTablesWithKeys <- actualNumberOfTablesWithKeys + 1
}
}
}
expect_equal(expectedNumberOfTablesWithKeys,actualNumberOfTablesWithKeys)
})
test_that("createRDBESDataObject can create an object from a H1 data extract
with the right number of rows, when CL has partially quoted vessel identifiers (issue #210)", {
# Test related to following issue
#https://github.com/ices-tools-dev/RDBEScore/issues/210
csvFilesH1 <- paste0(dirH1, "BadVesselIdentifiers/")
print(csvFilesH1)
myH1 <- createRDBESDataObject(input = csvFilesH1)
print(myH1)
# Get the default file names
fileNames <- RDBEScore::DefaultFileNames
# Remove any unnecessary files
fileNames[!names(fileNames) %in% c("CL")] <- NULL
# Append the right path
fileNames <-lapply(fileNames, function(x){paste(csvFilesH1,x,".csv",sep="")})
# Read the number of rows in each file
fileNumberOfRows <- lapply(fileNames, function(x){length(readLines(x))-1})
# For each file
for(x in names(fileNumberOfRows)){
# check if the value of nrow is equal to the length of readlines()-1
expect_true(nrow(myH1[[x]]) == fileNumberOfRows[x])
}
})
# Test list of dfs ---------------------------------------------------------
# Create list of dfs for comparison
list_with_nulls <- createRDBESDataObject(paste0(dirH1, "H1_Example.zip"))
list_of_dfs <- list_with_nulls[!(sapply(list_with_nulls, is.null))]
list_of_dfs <- lapply(list_of_dfs, as.data.frame)
colMapping <- stats::setNames(mapColNamesFieldR$Field.Name, mapColNamesFieldR$R.Name)
list_of_dfs_long_names <- lapply(list_of_dfs, function(df, colMapping){
colnames(df) <- colMapping[colnames(df)]
df
}, colMapping)
# convert list_of_dfs and list_of_dfs_long_names to lists of data.tables
list_of_dts <- lapply(list_of_dfs, as.data.table)
list_of_dts_long_names <- lapply(list_of_dfs_long_names, as.data.table)
test_that("Importing list of dfs works",{
genObj <- suppressWarnings(createRDBESDataObject(list_of_dfs, castToCorrectDataTypes = FALSE))
expect_equal(genObj, expObjH1)
})
test_that("Importing list of data.tables works",{
genObj <- suppressWarnings(createRDBESDataObject(list_of_dts, castToCorrectDataTypes = FALSE))
expect_equal(genObj, expObjH1)
})
test_that("Long column names are converted to R names (using list of data frames as input)",{
genObj <- suppressWarnings(createRDBESDataObject(list_of_dfs_long_names, castToCorrectDataTypes = FALSE))
expect_equal(genObj, expObjH1)
})
test_that("Long column names are converted to R names (using list of data tables as input)",{
genObj <- suppressWarnings(createRDBESDataObject(list_of_dts_long_names, castToCorrectDataTypes = FALSE))
expect_equal(genObj, expObjH1)
})
test_that("Extra column names are ignored (using list of data frames as input)",{
colnames(list_of_dfs_long_names[["VS"]])[27] <- "wrong"
genObj <- suppressWarnings(createRDBESDataObject(list_of_dfs_long_names, castToCorrectDataTypes = FALSE, strict=FALSE))
colnames(expObjH1[["VS"]])[27] <- "wrong"
expect_equal(genObj, expObjH1)
})
test_that("Extra column names are ignored (using list of data tables as input)",{
colnames(list_of_dts_long_names[["VS"]])[27] <- "wrong"
genObj <- suppressWarnings(createRDBESDataObject(list_of_dts_long_names, castToCorrectDataTypes = FALSE, strict=FALSE))
colnames(expObjH1[["VS"]])[27] <- "wrong"
expect_equal(genObj, expObjH1)
})
test_that("Importing list of dfs with castToCorrectDataTypes = TRUE works",{
genObj <- suppressWarnings(createRDBESDataObject(list_of_dfs, castToCorrectDataTypes = TRUE))
myDiffs <- validateRDBESDataObjectDataTypes(genObj)
numberOfDifferences <- nrow(myDiffs)
expect_equal(numberOfDifferences,0)
})
test_that("Importing list of data tables with castToCorrectDataTypes = TRUE works",{
genObj <- suppressWarnings(createRDBESDataObject(list_of_dts, castToCorrectDataTypes = TRUE))
myDiffs <- validateRDBESDataObjectDataTypes(genObj)
numberOfDifferences <- nrow(myDiffs)
expect_equal(numberOfDifferences,0)
})
test_that("Importing list of dfs with different names than the ones requested does not work",{
names(list_of_dfs)[1] <- "Design"
expect_error(expect_warning(createRDBESDataObject(list_of_dfs, castToCorrectDataTypes = FALSE),
"NOTE: Creating RDBES data objects from a list of local data frames or data.tables bypasses the RDBES upload data integrity checks.\n"),
"You have given list names that are not valid:\nDesign")
})
test_that("Importing list of data.tables with different names than the ones requested does not work",{
names(list_of_dts)[1] <- "Design"
expect_error(expect_warning(createRDBESDataObject(list_of_dts, castToCorrectDataTypes = FALSE),
"NOTE: Creating RDBES data objects from a list of local data frames or data.tables bypasses the RDBES upload data integrity checks.\n"),
"You have given list names that are not valid:\nDesign")
})
test_that("Importing list of dfs with duplicate table names does not work",{
names(list_of_dfs)[1] <- "DE"
names(list_of_dfs)[2] <- "DE"
expect_error(expect_warning(createRDBESDataObject(list_of_dfs, castToCorrectDataTypes = FALSE), "NOTE: Creating RDBES data objects from a list of local data frames or data.tables bypasses the RDBES upload data integrity checks.\n"),
"You have given list names that have duplicate table names:\nDE")
})
test_that("Importing list of data.tables with duplicate table names does not work",{
names(list_of_dts)[1] <- "DE"
names(list_of_dts)[2] <- "DE"
expect_error(expect_warning(createRDBESDataObject(list_of_dts, castToCorrectDataTypes = FALSE), "NOTE: Creating RDBES data objects from a list of local data frames or data.tables bypasses the RDBES upload data integrity checks.\n"),
"You have given list names that have duplicate table names:\nDE")
})
test_that("Importing list of dfs with different names than the ones requested & duplicate table names does not work",{
names(list_of_dfs)[1] <- "Design"
names(list_of_dfs)[2] <- "DE"
names(list_of_dfs)[3] <- "DE"
expect_error(expect_warning(createRDBESDataObject(list_of_dfs,
castToCorrectDataTypes = FALSE),
"NOTE: Creating RDBES data objects from a list of local data frames or data.tables bypasses the RDBES upload data integrity checks."),
"You have given list names that are not valid:\nDesign")
})
test_that("Importing list of data.tables with different names than the ones requested & duplicate table names does not work",{
names(list_of_dts)[1] <- "Design"
names(list_of_dts)[2] <- "DE"
names(list_of_dts)[3] <- "DE"
expect_error(expect_warning(createRDBESDataObject(list_of_dts,
castToCorrectDataTypes = FALSE),
"NOTE: Creating RDBES data objects from a list of local data frames or data.tables bypasses the RDBES upload data integrity checks."),
"You have given list names that are not valid:\nDesign")
})
test_that("Importing multiple lists does not work",{
list1 <- list_of_dfs
list2 <- list_of_dfs
expect_error(expect_warning(createRDBESDataObject(input = c(list1, list2),
castToCorrectDataTypes = FALSE),
"NOTE: Creating RDBES data objects from a list of local data frames or data.tables bypasses the RDBES upload data integrity checks.\n"),
"You have given list names that have duplicate table names:\nDE, SD, VS, FT, FO, SS, SA, FM, BV, VD, SL")
})
test_that("Importing dataframe does not work",{
df <- as.data.frame(list_of_dfs[["DE"]])
expect_error(createRDBESDataObject(input = df,
castToCorrectDataTypes = FALSE),
"Input type not recognised. Should be a RDBES zip file, folder of csv files, or list of data frames.")
})
test_that("Giving an empty dataframe within the list does not work",{
list_with_nulls <- lapply(list_with_nulls, as.data.frame)
expect_error(expect_warning(createRDBESDataObject(input = list_with_nulls, castToCorrectDataTypes = FALSE),
"NOTE: Creating RDBES data objects from a list of local data frames bypasses the RDBES upload data integrity checks.\n"),
"id does not exist in the input tables.")
})
}) ## end capture.output
ices-tools-dev/icesRDBES documentation built on April 17, 2025, 1:58 p.m.
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capture.output({ ## suppresses printing of console output when running test()
# common parameters
# H1 directory
dirH1 <- "./h1_v_20250211/"
# H5 directory
dirH5 <- "./h5_v_20250211/"
# H7 directory
dirH7 <- "./h7_v_1_19_26/"
# H1 object for comparison
expObjH1 <- H1Example
# Test general behavior --------------------------------------------------
test_that("createRDBESDataObject will give a warning if given a dir with no relevant files in it", {
myPath <- "."
expect_warning(createRDBESDataObject(input = myPath),"No relevant files found in given directory - an empty object will be created")
})
test_that("Expect warning when the input is not csv, list of dfs, zip files, NULL - Test Integer input", {
myPath <- as.integer(1)
expect_error(createRDBESDataObject(myPath), "Input type not recognised. Should be a RDBES zip file, folder of csv files, or list of data frames.")
})
test_that("Expect warning when the input is not csv, list of dfs, zip files, NULL - Test dataframe input", {
myPath <- as.data.frame(1)
expect_error(createRDBESDataObject(myPath), "Input type not recognised. Should be a RDBES zip file, folder of csv files, or list of data frames.")
})
test_that("createRDBESDataObject will throw an error when given multiple inputs", {
zipFiles <- c(
"H1_Example.zip"
)
H1 <- paste0(dirH1, zipFiles)
df <- as.data.frame(1)
expect_error(createRDBESDataObject(input = c(H1, df, dirH1)), "Input type not recognised. Should be a RDBES zip file, folder of csv files, or list of data frames.")
})
# Test ZIP inputs ---------------------------------------------------------
test_that("importing foldered zipped H1 example data works", {
zipFiles <- c(
"H1_Example_fd.zip"
)
genObj <- createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE)
expect_equal(genObj, expObjH1)
})
test_that("importing foldered zipped H1 and H2 gives an error", {
zipFiles <- c(
"H1_H2_Example_fd.zip"
)
genObj <- expect_error(
createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE),
"The zip file contains multiple hierarchies.\nTo import a selected hierarchy, please provide the hierarchy as an argument e.g like:\nHierachy = 1"
)
})
test_that("importing foldered zipped H1 and H2 example data works when hierarchy is specified", {
zipFiles <- c(
"H1_H2_Example_fd.zip"
)
genObj <- createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE,
Hierarchy = 1)
expect_equal(genObj, expObjH1)
})
test_that("importing foldered zipped H1 and H2 example does not work when hierarchy is misspecified", {
zipFiles <- c(
"H1_H2_Example_fd.zip"
)
genObj <- expect_error(
createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE,
Hierarchy = "H1"),
"The zip file does not contain the hierarchy specified. The options are: 1, 2\nPlease provide a valid hierarchy as an argument. e.g like:\nHierachy = 1"
)
})
test_that("importing zipped H1 example data works", {
zipFiles <- c(
"H1_Example.zip"
)
genObj <- createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE)
expect_equal(genObj, expObjH1)
})
test_that("importing some data that is not zipped with some data that are zipped H1 example data should not work", {
zipFiles <- c(
"H1_Example.zip",
"HSL_Example.zip",
"VesselDetails.csv"
)
genObj <- expect_error(
createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE),
"You cannot import a mix of 'csv' and 'zip' inputs. To import multiple tables unzip all files and import as a folder of 'csv' files."
)
})
test_that("importing subset H1 example data works", {
zipFiles <- c(
"HSL_Example.zip",
"HVD_Example.zip"
)
genObj <- createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE)
expect_equal(genObj$VD, expObjH1$VD)
expect_equal(genObj$SS, NULL)
expect_equal(genObj$SL, expObjH1$SL)
})
test_that("Overwriting a table from a zip file produces a warning", {
zipFiles <- c(
"H1_Example.zip",
"HVD_Example.zip")
expect_warning(
createRDBESDataObject(paste0(dirH1, zipFiles),
castToCorrectDataTypes = FALSE),
"Duplicate unzipped files detected:\n")
})
test_that("The order of importing should not matter", {
zipFiles1 <- c(
"H1_Example.zip",
"HVD_Example.zip")
genObj1 <- suppressWarnings(
createRDBESDataObject(paste0(dirH1, zipFiles1),
castToCorrectDataTypes = TRUE))
zipFiles2 <- c("HVD_Example.zip",
"H1_Example.zip")
genObj2 <- suppressWarnings(
createRDBESDataObject(paste0(dirH1, zipFiles2),
castToCorrectDataTypes = TRUE))
expect_equal(genObj1$VD, genObj2$VD)
expect_equal(genObj1$SS, genObj2$SS)
expect_equal(genObj1$SL, genObj2$SL)
expect_equal(genObj1$FT, genObj2$FT)
expect_equal(genObj1, genObj2)
})
test_that("createRDBESDataObject creates an object with the correct data types", {
zipFiles <- c(
"H1_Example.zip",
"HVD_Example.zip")
genObj <- suppressWarnings(createRDBESDataObject(input = paste0(dirH1, zipFiles),
castToCorrectDataTypes = TRUE))
myDiffs <- validateRDBESDataObjectDataTypes(genObj)
numberOfDifferences <- nrow(myDiffs)
expect_equal(numberOfDifferences,0)
})
# Test CSV inputs ---------------------------------------------------------
test_that("createRDBESDataObject can create an object from a H1 data extract
without errors or warnings", {
csvFilesH1 <- dirH1
expect_warning(createRDBESDataObject(input = csvFilesH1), NA)
expect_error(createRDBESDataObject(input = csvFilesH1), NA)
})
test_that("createRDBESDataObject can create an object from a H1 data extract
without errors or warnings (when castToCorrectDataTypes = FALSE)", {
csvFilesH1 <- dirH1
expect_warning(
createRDBESDataObject(input = csvFilesH1,
castToCorrectDataTypes = FALSE), NA)
expect_error(
createRDBESDataObject(input = csvFilesH1,
castToCorrectDataTypes = FALSE), NA)
})
test_that("createRDBESDataObject can create an object from a H1 data extract
with the right number of rows", {
csvFilesH1 <- dirH1
myH1 <- createRDBESDataObject(input = csvFilesH1)
# Get the default file names
fileNames <- RDBEScore::DefaultFileNames
# Remove any unnecessary files
fileNames[names(fileNames) %in% c("TE","LO","OS","LE")] <- NULL
# Append the right path
fileNames <-lapply(fileNames, function(x){paste(csvFilesH1,x,".csv",sep="")})
# Read the number of rows in each file
fileNumberOfRows <- lapply(fileNames, function(x){length(readLines(x))-1})
# For each file
for(x in names(fileNumberOfRows)){
# check if the value of nrow is equal to the length of readlines()-1
expect_true(nrow(myH1[[x]]) == fileNumberOfRows[x])
}
})
test_that("createRDBESDataObject can create an object from an H5 data extract
without errors or warnings", {
csvFilesH5 <- dirH5
expect_warning(createRDBESDataObject(input = csvFilesH5), NA)
expect_error(createRDBESDataObject(input = csvFilesH5), NA)
})
test_that("createRDBESDataObject can create an object from an H5 data extract
without errors or warnings (when castToCorrectDataTypes = FALSE)", {
csvFilesH5 <- dirH5
expect_warning(
createRDBESDataObject(input = csvFilesH5,
castToCorrectDataTypes = FALSE), NA)
expect_error(
createRDBESDataObject(input = csvFilesH5,
castToCorrectDataTypes = FALSE), NA)
})
test_that("createRDBESDataObject can create an object from a H5 data extract
with the right number of rows", {
csvFilesH5 <- dirH5
myH5 <- createRDBESDataObject(input = csvFilesH5)
# Get the default file names
fileNames <- RDBEScore::DefaultFileNames
# Remove any unnecessary files
fileNames[names(fileNames) %in% c("TE","LO","VS","FO")] <- NULL
# Append the right path
fileNames <-lapply(fileNames, function(x){paste(csvFilesH5,x,".csv",sep="")})
# Read the number of rows in each file
fileNumberOfRows <- lapply(fileNames, function(x){length(readLines(x))-1})
# For each file
for(x in names(fileNumberOfRows)){
# check if the value of nrow is equal to the length of readlines()-1
expect_true(nrow(myH5[[x]]) == fileNumberOfRows[x])
}
})
test_that("createRDBESDataObject can create an object from an H1 data extract by specifying file names without errors or warnings", {
csvFilesH1 <- dirH1
myFileNames <- list("DE"="DE.csv","SD"="SD.csv")
myObject <- expect_warning(createRDBESDataObject(input = csvFilesH1, listOfFileNames = myFileNames), NA)
myObject <- expect_error(createRDBESDataObject(input = csvFilesH1, listOfFileNames = myFileNames), NA)
})
test_that("createRDBESDataObject returns warning when input = NULL & the listofFileNames is not", {
csvFilesH1 <- NULL
myFileNames <- list("DE"="DE.csv","SD"="SD.csv")
expect_warning(createRDBESDataObject(input = csvFilesH1, listOfFileNames = myFileNames), NA)
})
test_that("createRDBESDataObject creates an object with the correct data types", {
csvFilesH1 <- dirH1
myRDBESDataObject <- createRDBESDataObject(input = csvFilesH1,
castToCorrectDataTypes = TRUE)
myDiffs <- validateRDBESDataObjectDataTypes(myRDBESDataObject)
numberOfDifferences <- nrow(myDiffs)
expect_equal(numberOfDifferences,0)
})
test_that("createRDBESDataObject creates an H1 object with keys on the data tables", {
csvFilesH1 <- dirH1
myRDBESDataObject <- createRDBESDataObject(input = csvFilesH1)
# Not all of the RDBES table types are in the sample data
expectedNumberOfTablesWithKeys <- 14
actualNumberOfTablesWithKeys <- 0
for(aTable in names(myRDBESDataObject)){
if ('data.table' %in% class(myRDBESDataObject[[aTable]])){
if (!is.null(data.table::key(myRDBESDataObject[[aTable]]))){
actualNumberOfTablesWithKeys <- actualNumberOfTablesWithKeys + 1
}
}
}
expect_equal(expectedNumberOfTablesWithKeys,actualNumberOfTablesWithKeys)
})
test_that("createRDBESDataObject creates an H5 object with keys on the data tables", {
csvFilesH5 <- dirH5
myRDBESDataObject <- createRDBESDataObject(input = csvFilesH5)
# Not all of the RDBES table types are in the sample data
expectedNumberOfTablesWithKeys <- 14
actualNumberOfTablesWithKeys <- 0
for(aTable in names(myRDBESDataObject)){
if ('data.table' %in% class(myRDBESDataObject[[aTable]])){
if (!is.null(data.table::key(myRDBESDataObject[[aTable]]))){
actualNumberOfTablesWithKeys <- actualNumberOfTablesWithKeys + 1
}
}
}
expect_equal(expectedNumberOfTablesWithKeys,actualNumberOfTablesWithKeys)
})
test_that("createRDBESDataObject creates an H7 object with keys on the data tables", {
csvFilesH7 <- dirH7
myRDBESDataObject <- createRDBESDataObject(input = csvFilesH7)
# Not all of the RDBES table types are in the sample data
expectedNumberOfTablesWithKeys <- 13
actualNumberOfTablesWithKeys <- 0
for(aTable in names(myRDBESDataObject)){
if ('data.table' %in% class(myRDBESDataObject[[aTable]])){
if (!is.null(data.table::key(myRDBESDataObject[[aTable]]))){
actualNumberOfTablesWithKeys <- actualNumberOfTablesWithKeys + 1
}
}
}
expect_equal(expectedNumberOfTablesWithKeys,actualNumberOfTablesWithKeys)
})
test_that("createRDBESDataObject can create an object from a H1 data extract
with the right number of rows, when CL has partially quoted vessel identifiers (issue #210)", {
# Test related to following issue
#https://github.com/ices-tools-dev/RDBEScore/issues/210
csvFilesH1 <- paste0(dirH1, "BadVesselIdentifiers/")
print(csvFilesH1)
myH1 <- createRDBESDataObject(input = csvFilesH1)
print(myH1)
# Get the default file names
fileNames <- RDBEScore::DefaultFileNames
# Remove any unnecessary files
fileNames[!names(fileNames) %in% c("CL")] <- NULL
# Append the right path
fileNames <-lapply(fileNames, function(x){paste(csvFilesH1,x,".csv",sep="")})
# Read the number of rows in each file
fileNumberOfRows <- lapply(fileNames, function(x){length(readLines(x))-1})
# For each file
for(x in names(fileNumberOfRows)){
# check if the value of nrow is equal to the length of readlines()-1
expect_true(nrow(myH1[[x]]) == fileNumberOfRows[x])
}
})
# Test list of dfs ---------------------------------------------------------
# Create list of dfs for comparison
list_with_nulls <- createRDBESDataObject(paste0(dirH1, "H1_Example.zip"))
list_of_dfs <- list_with_nulls[!(sapply(list_with_nulls, is.null))]
list_of_dfs <- lapply(list_of_dfs, as.data.frame)
colMapping <- stats::setNames(mapColNamesFieldR$Field.Name, mapColNamesFieldR$R.Name)
list_of_dfs_long_names <- lapply(list_of_dfs, function(df, colMapping){
colnames(df) <- colMapping[colnames(df)]
df
}, colMapping)
# convert list_of_dfs and list_of_dfs_long_names to lists of data.tables
list_of_dts <- lapply(list_of_dfs, as.data.table)
list_of_dts_long_names <- lapply(list_of_dfs_long_names, as.data.table)
test_that("Importing list of dfs works",{
genObj <- suppressWarnings(createRDBESDataObject(list_of_dfs, castToCorrectDataTypes = FALSE))
expect_equal(genObj, expObjH1)
})
test_that("Importing list of data.tables works",{
genObj <- suppressWarnings(createRDBESDataObject(list_of_dts, castToCorrectDataTypes = FALSE))
expect_equal(genObj, expObjH1)
})
test_that("Long column names are converted to R names (using list of data frames as input)",{
genObj <- suppressWarnings(createRDBESDataObject(list_of_dfs_long_names, castToCorrectDataTypes = FALSE))
expect_equal(genObj, expObjH1)
})
test_that("Long column names are converted to R names (using list of data tables as input)",{
genObj <- suppressWarnings(createRDBESDataObject(list_of_dts_long_names, castToCorrectDataTypes = FALSE))
expect_equal(genObj, expObjH1)
})
test_that("Extra column names are ignored (using list of data frames as input)",{
colnames(list_of_dfs_long_names[["VS"]])[27] <- "wrong"
genObj <- suppressWarnings(createRDBESDataObject(list_of_dfs_long_names, castToCorrectDataTypes = FALSE, strict=FALSE))
colnames(expObjH1[["VS"]])[27] <- "wrong"
expect_equal(genObj, expObjH1)
})
test_that("Extra column names are ignored (using list of data tables as input)",{
colnames(list_of_dts_long_names[["VS"]])[27] <- "wrong"
genObj <- suppressWarnings(createRDBESDataObject(list_of_dts_long_names, castToCorrectDataTypes = FALSE, strict=FALSE))
colnames(expObjH1[["VS"]])[27] <- "wrong"
expect_equal(genObj, expObjH1)
})
test_that("Importing list of dfs with castToCorrectDataTypes = TRUE works",{
genObj <- suppressWarnings(createRDBESDataObject(list_of_dfs, castToCorrectDataTypes = TRUE))
myDiffs <- validateRDBESDataObjectDataTypes(genObj)
numberOfDifferences <- nrow(myDiffs)
expect_equal(numberOfDifferences,0)
})
test_that("Importing list of data tables with castToCorrectDataTypes = TRUE works",{
genObj <- suppressWarnings(createRDBESDataObject(list_of_dts, castToCorrectDataTypes = TRUE))
myDiffs <- validateRDBESDataObjectDataTypes(genObj)
numberOfDifferences <- nrow(myDiffs)
expect_equal(numberOfDifferences,0)
})
test_that("Importing list of dfs with different names than the ones requested does not work",{
names(list_of_dfs)[1] <- "Design"
expect_error(expect_warning(createRDBESDataObject(list_of_dfs, castToCorrectDataTypes = FALSE),
"NOTE: Creating RDBES data objects from a list of local data frames or data.tables bypasses the RDBES upload data integrity checks.\n"),
"You have given list names that are not valid:\nDesign")
})
test_that("Importing list of data.tables with different names than the ones requested does not work",{
names(list_of_dts)[1] <- "Design"
expect_error(expect_warning(createRDBESDataObject(list_of_dts, castToCorrectDataTypes = FALSE),
"NOTE: Creating RDBES data objects from a list of local data frames or data.tables bypasses the RDBES upload data integrity checks.\n"),
"You have given list names that are not valid:\nDesign")
})
test_that("Importing list of dfs with duplicate table names does not work",{
names(list_of_dfs)[1] <- "DE"
names(list_of_dfs)[2] <- "DE"
expect_error(expect_warning(createRDBESDataObject(list_of_dfs, castToCorrectDataTypes = FALSE), "NOTE: Creating RDBES data objects from a list of local data frames or data.tables bypasses the RDBES upload data integrity checks.\n"),
"You have given list names that have duplicate table names:\nDE")
})
test_that("Importing list of data.tables with duplicate table names does not work",{
names(list_of_dts)[1] <- "DE"
names(list_of_dts)[2] <- "DE"
expect_error(expect_warning(createRDBESDataObject(list_of_dts, castToCorrectDataTypes = FALSE), "NOTE: Creating RDBES data objects from a list of local data frames or data.tables bypasses the RDBES upload data integrity checks.\n"),
"You have given list names that have duplicate table names:\nDE")
})
test_that("Importing list of dfs with different names than the ones requested & duplicate table names does not work",{
names(list_of_dfs)[1] <- "Design"
names(list_of_dfs)[2] <- "DE"
names(list_of_dfs)[3] <- "DE"
expect_error(expect_warning(createRDBESDataObject(list_of_dfs,
castToCorrectDataTypes = FALSE),
"NOTE: Creating RDBES data objects from a list of local data frames or data.tables bypasses the RDBES upload data integrity checks."),
"You have given list names that are not valid:\nDesign")
})
test_that("Importing list of data.tables with different names than the ones requested & duplicate table names does not work",{
names(list_of_dts)[1] <- "Design"
names(list_of_dts)[2] <- "DE"
names(list_of_dts)[3] <- "DE"
expect_error(expect_warning(createRDBESDataObject(list_of_dts,
castToCorrectDataTypes = FALSE),
"NOTE: Creating RDBES data objects from a list of local data frames or data.tables bypasses the RDBES upload data integrity checks."),
"You have given list names that are not valid:\nDesign")
})
test_that("Importing multiple lists does not work",{
list1 <- list_of_dfs
list2 <- list_of_dfs
expect_error(expect_warning(createRDBESDataObject(input = c(list1, list2),
castToCorrectDataTypes = FALSE),
"NOTE: Creating RDBES data objects from a list of local data frames or data.tables bypasses the RDBES upload data integrity checks.\n"),
"You have given list names that have duplicate table names:\nDE, SD, VS, FT, FO, SS, SA, FM, BV, VD, SL")
})
test_that("Importing dataframe does not work",{
df <- as.data.frame(list_of_dfs[["DE"]])
expect_error(createRDBESDataObject(input = df,
castToCorrectDataTypes = FALSE),
"Input type not recognised. Should be a RDBES zip file, folder of csv files, or list of data frames.")
})
test_that("Giving an empty dataframe within the list does not work",{
list_with_nulls <- lapply(list_with_nulls, as.data.frame)
expect_error(expect_warning(createRDBESDataObject(input = list_with_nulls, castToCorrectDataTypes = FALSE),
"NOTE: Creating RDBES data objects from a list of local data frames bypasses the RDBES upload data integrity checks.\n"),
"id does not exist in the input tables.")
})
}) ## end capture.output
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