Nothing
tests/testthat/test-list.R
In ProjectTemplate: Automates the Creation of New Statistical Analysis Projects
context('List data')
temp_csv_file <- function(dir = '') {
gsub('^[/\\\\]', '', tempfile(pattern = "file", tmpdir = dir, fileext = ".csv"))
}
test_that('available data is listed correctly with default configuration', {
# Create temporary project
test_project <- tempfile('test_project')
suppressMessages(create.project(test_project))
on.exit(unlink(test_project, recursive = TRUE), add = TRUE)
# Set temporary project as working directory
oldwd <- setwd(test_project)
on.exit(setwd(oldwd), add = TRUE)
# Clear the global environment
clear()
# Create some test data so the file can be loaded if not ignored
test_data <- data.frame(Names = c("a", "b", "c"), Ages = c(20, 30, 40))
# Build two temporary filenames, strip leading /
test_file1 <- temp_csv_file()
test_file2 <- temp_csv_file(dir = 'test')
# Write test data to files
write.csv(test_data, file = file.path('data', test_file1), row.names = FALSE)
dir.create('data/test')
write.csv(test_data, file = file.path('data', test_file2), row.names = FALSE)
# Check if list.data can be called and returns a data.frame
expect_error(data.files <- list.data(), NA)
expect_true(is.data.frame(data.files))
# Check data.frame has a character variable "filename"
expect_true("filename" %in% names(data.files))
expect_true(class(data.files$filename) == "character")
# Check data.frame has a character variable "varname"
expect_true("varname" %in% names(data.files))
expect_true(class(data.files$varname) == "character")
# Check data.frame has a list variable "reader"
expect_true("reader" %in% names(data.files))
expect_true(class(data.files$reader) == "list")
# Check data.frame has a logical variable "is_ignored"
expect_true("is_ignored" %in% names(data.files))
expect_true(class(data.files$is_ignored) == "logical")
# Check data.frame has a logical variable "is_directory"
expect_true("is_directory" %in% names(data.files))
expect_true(class(data.files$is_directory) == "logical")
# Check data.frame has a logical variable "is_cached"
expect_true("is_cached" %in% names(data.files))
expect_true(class(data.files$is_cached) == "logical")
# Check data.frame has a logical variable "cache_only"
expect_true("cache_only" %in% names(data.files))
expect_true(class(data.files$cache_only) == "logical")
# Check if data.frame has three rows with default config:
# - fileXXXXX.csv (test_file1, not ignored, varname: fileXXXXX, reader: csv.reader)
# - README.md (not ignored, varname: "", reader: "")
# - test (subdirectory, not ignored, varname: "", reader: "")
expect_true(nrow(data.files) == 3)
test.df <- data.frame(
filename = c(test_file1, 'README.md', 'test'),
varname = c(gsub('.csv', '', test_file1), "", ""),
is_ignored = c(FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, TRUE),
is_cached = c(FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
test.df$reader <- list('csv.reader', '', '')
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$varname, test.df$varname)
expect_equal(data.files$reader, test.df$reader)
expect_equal(data.files$is_ignored, test.df$is_ignored)
expect_equal(data.files$is_directory, test.df$is_directory)
expect_equal(data.files$is_cached, test.df$is_cached)
expect_equal(data.files$cache_only, test.df$cache_only)
})
test_that('available data is listed correctly with recursive_loading = TRUE', {
# Create temporary project
test_project <- tempfile('test_project')
suppressMessages(create.project(test_project))
on.exit(unlink(test_project, recursive = TRUE), add = TRUE)
# Set temporary project as working directory
oldwd <- setwd(test_project)
on.exit(setwd(oldwd), add = TRUE)
# Read the config data and set cache_loaded_data to FALSE
config <- .read.config()
expect_error(config$recursive_loading <- TRUE, NA)
.save.config(config)
# Create some test data so the file can be loaded if not ignored
test_data <- data.frame(Names = c("a", "b", "c"), Ages = c(20, 30, 40))
# Build two temporary filenames, strip leading /
test_file1 <- temp_csv_file()
test_file2 <- temp_csv_file(dir = 'test')
# Write test data to files
write.csv(test_data, file = file.path('data', test_file1), row.names = FALSE)
dir.create('data/test')
write.csv(test_data, file = file.path('data', test_file2), row.names = FALSE)
# Setup test data.frame
test.df <- data.frame(
filename = c(test_file1, 'README.md', gsub("\\\\", "/", test_file2)),
varname = c(gsub('.csv', '', test_file1),
"",
gsub('[/\\\\]', '.', gsub('.csv', '', test_file2))),
is_ignored = c(FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, FALSE),
is_cached = c(FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
test.df$reader <- list("csv.reader", "", "csv.reader")
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
# Check if list.data can be called and returns a data.frame
expect_error(data.files <- list.data(), NA)
# Check if data.frame has three rows with default config:
# - fileXXXXX.csv (test_file1)
# - README.md
# - test/fileYYYYYY.csv (test_file2)
expect_true(nrow(data.files) == 3)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$varname, test.df$varname)
expect_equal(data.files$reader, test.df$reader)
expect_equal(data.files$is_directory, test.df$is_directory)
})
test_that('available data is listed correctly with data_ignore', {
# Create temporary project
test_project <- tempfile('test_project')
suppressMessages(create.project(test_project))
on.exit(unlink(test_project, recursive = TRUE), add = TRUE)
# Set temporary project as working directory
oldwd <- setwd(test_project)
on.exit(setwd(oldwd), add = TRUE)
# Create some test data so the file can be loaded if not ignored
test_data <- data.frame(Names = c("a", "b", "c"), Ages = c(20, 30, 40))
# Build two temporary filenames, strip leading /
test_file1 <- temp_csv_file()
test_file2 <- temp_csv_file(dir = 'test')
# Write test data to files
write.csv(test_data, file = file.path('data', test_file1), row.names = FALSE)
dir.create('data/test')
write.csv(test_data, file = file.path('data', test_file2), row.names = FALSE)
# Write an empty Thumbs.db that cannot be loaded by RSQLite
writeLines('\n', file.path('data', 'Thumbs.db'))
# Check if data.frame has four rows with default config:
# - fileXXXXX.csv (test_file1, not ignored)
# - README.md (not ignored)
# - test (subdirectory, not ignored)
# - Thumbs.db (ignored)
test.df <- data.frame(
filename = c(test_file1, 'README.md', 'test', 'Thumbs.db'),
varname = c(gsub('.csv', '', test_file1), "", "", ""),
reader = c("csv.reader", "", "", ""),
is_ignored = c(FALSE, FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, TRUE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_error(data.files <- list.data(), NA)
expect_true(nrow(data.files) == 4)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_ignored, test.df$is_ignored)
# Check empty data_ignore:
# - fileXXXXX.csv (test_file1, not ignored)
# - README.md (not ignored)
# - test/fileYYYYY.csv (test_file2, not ignored)
# - Thumbs.db (not ignored)
test.df <- data.frame(
filename = c(test_file1, 'README.md', gsub("\\\\", "/", test_file2), 'Thumbs.db'),
varname = c(gsub('.csv', '', test_file1),
"",
gsub('[/\\\\]', '.', gsub('.csv', '', test_file2)),
""),
reader = c("csv.reader", "", "csv.reader", ""),
is_ignored = c(FALSE, FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, FALSE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_error(data.files <- list.data(data_ignore = '',
recursive_loading = TRUE), NA)
expect_true(nrow(data.files) == 4)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_ignored, test.df$is_ignored)
# Check wildcard ignore "*.csv":
# - fileXXXXX.csv (test_file1, ignored)
# - README.md (not ignored)
# - test (subdirectory, not ignored)
# - Thumbs.db (not ignored)
test.df <- data.frame(
filename = c(test_file1, 'README.md', 'test', 'Thumbs.db'),
varname = c(gsub('.csv', '', test_file1), "", "", ""),
reader = c("csv.reader", "", "", ""),
is_ignored = c(TRUE, FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, TRUE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_error(data.files <- list.data(data_ignore = '*.csv'), NA)
expect_true(nrow(data.files) == 4)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_ignored, test.df$is_ignored)
# Check wildcard ignore "*.csv" with recursive loading on:
# - fileXXXXX.csv (test_file1, ignored)
# - README.md (not ignored)
# - test/fileYYYYY.csv (test_file2, not ignored)
# - Thumbs.db (not ignored)
test.df <- data.frame(
filename = c(test_file1, 'README.md', gsub("\\\\", "/", test_file2), 'Thumbs.db'),
varname = c(gsub('.csv', '', test_file1),
"",
gsub('[/\\\\]', '.', gsub('.csv', '', test_file2)),
""),
reader = c("csv.reader", "", "csv.reader", ""),
is_ignored = c(TRUE, FALSE, TRUE, FALSE),
is_directory = c(FALSE, FALSE, FALSE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_error(data.files <- list.data(data_ignore = '*.csv',
recursive_loading = TRUE), NA)
expect_true(nrow(data.files) == 4)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_ignored, test.df$is_ignored)
# Check regular expression ignore "^\w*.csv", only match csv in data, not in
# subdirectories:
# - fileXXXXX.csv (test_file1, ignored)
# - README.md (not ignored)
# - test/fileYYYYY.csv (test_file2, not ignored)
# - Thumbs.db (not ignored)
test.df <- data.frame(
filename = c(test_file1, 'README.md', gsub("\\\\", "/", test_file2), 'Thumbs.db'),
varname = c(gsub('.csv', '', test_file1),
"",
gsub('[/\\\\]', '.', gsub('.csv', '', test_file2)),
""),
reader = c("csv.reader", "", "csv.reader", ""),
is_ignored = c(TRUE, FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, FALSE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_error(data.files <- list.data(data_ignore = '/^\\w*\\.csv/',
recursive_loading = TRUE), NA)
expect_true(nrow(data.files) == 4)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_ignored, test.df$is_ignored)
# Check combination literal filename "Thumbs.db" and regular expression
# ignore "^\w*.csv", only match csv in data, not in subdirectories:
# - fileXXXXX.csv (test_file1, ignored)
# - README.md (not ignored)
# - test/fileYYYYY.csv (test_file2, not ignored)
# - Thumbs.db (ignored)
test.df <- data.frame(
filename = c(test_file1, 'README.md', gsub("\\\\", "/", test_file2), 'Thumbs.db'),
varname = c(gsub('.csv', '', test_file1),
"",
gsub('[/\\\\]', '.', gsub('.csv', '', test_file2)),
""),
reader = c("csv.reader", "", "csv.reader", ""),
is_ignored = c(TRUE, FALSE, FALSE, TRUE),
is_directory = c(FALSE, FALSE, FALSE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_error(data.files <- list.data(data_ignore = 'Thumbs.db, /^\\w*\\.csv/',
recursive_loading = TRUE), NA)
expect_true(nrow(data.files) == 4)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_ignored, test.df$is_ignored)
# Check extra comma in combination literal filename "Thumbs.db" and regular
# expression ignore "^\w*\.csv", only match csv in data, not in
# subdirectories:
# - fileXXXXX.csv (test_file1, ignored)
# - README.md (not ignored)
# - test/fileYYYYY.csv (test_file2, not ignored)
# - Thumbs.db (ignored)
test.df <- data.frame(
filename = c(test_file1, 'README.md', gsub("\\\\", "/", test_file2), 'Thumbs.db'),
varname = c(gsub('.csv', '', test_file1),
"",
gsub('[/\\\\]', '.', gsub('.csv', '', test_file2)),
""),
reader = c("csv.reader", "", "csv.reader", ""),
is_ignored = c(TRUE, FALSE, FALSE, TRUE),
is_directory = c(FALSE, FALSE, FALSE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_error(data.files <- list.data(data_ignore = 'Thumbs.db,,/^\\w*\\.csv/',
recursive_loading = TRUE), NA)
expect_true(nrow(data.files) == 4)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_ignored, test.df$is_ignored)
})
test_that('cached data is listed correctly as already cached', {
# Create temporary project
test_project <- tempfile('test_project')
suppressMessages(create.project(test_project))
on.exit(unlink(test_project, recursive = TRUE), add = TRUE)
# Set temporary project as working directory
oldwd <- setwd(test_project)
on.exit(setwd(oldwd), add = TRUE)
# Clear the global environment
clear()
# Create some test data so the file can be loaded if not ignored
test_data <- data.frame(Names = c("a", "b", "c"), Ages = c(20, 30, 40))
# Build two temporary filenames
test_file1 <- temp_csv_file()
test_file2 <- temp_csv_file(dir = 'test')
# Write test data to files
write.csv(test_data, file = file.path('data', test_file1), row.names = FALSE)
dir.create('data/test')
write.csv(test_data, file = file.path('data', test_file2), row.names = FALSE)
expect_error(data.files <- list.data(), NA)
# Check if data.frame has three rows with default config:
# - fileXXXXX.csv (test_file1, not cached)
# - README.md (not ignored, not cached)
# - test (subdirectory, not cached)
test.df <- data.frame(
filename = c(test_file1, 'README.md', 'test'),
varname = c(gsub('.csv', '', test_file1), '', ''),
reader = c("csv.reader", "", ""),
is_ignored = c(FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, TRUE),
is_cached = c(FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_cached, test.df$is_cached)
# Load the project so variables are cached, then list data again
suppressMessages(load.project())
expect_error(data.files <- list.data(), NA)
# Check if data.frame has three rows with default config:
# - fileXXXXX.csv (test_file1, cached)
# - README.md (not ignored, not cached)
# - test (subdirectory, not cached)
test.df <- data.frame(
filename = c(test_file1, 'README.md', 'test'),
varname = c(gsub('.csv', '', test_file1), '', ''),
reader = c("csv.reader", "", ""),
is_ignored = c(FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, TRUE),
is_cached = c(TRUE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_cached, test.df$is_cached)
})
test_that('cached data created during munging listed as cached only', {
skip_if_not_installed("formatR")
# Create temporary project
test_project <- tempfile('test_project')
suppressMessages(create.project(test_project))
on.exit(unlink(test_project, recursive = TRUE), add = TRUE)
# Set temporary project as working directory
oldwd <- setwd(test_project)
on.exit(setwd(oldwd), add = TRUE)
# Clear the global environment
clear()
# Create some test data so the file can be loaded if not ignored
test_data <- data.frame(Names = c("a", "b", "c"), Ages = c(20, 30, 40))
# Build two temporary filenames
test_file1 <- temp_csv_file()
test_file2 <- temp_csv_file(dir = 'test')
# Write test data to files
write.csv(test_data, file = file.path('data', test_file1), row.names = FALSE)
dir.create('data/test')
write.csv(test_data, file = file.path('data', test_file2), row.names = FALSE)
# Cache a code fragment
cache(variable = "test_data", CODE = {
data.frame(Names = c("a", "b", "c"), Ages = c(20, 30, 40))
})
expect_error(data.files <- list.data(), NA)
# Check if data.frame has four rows with default config:
# - fileXXXXX.csv (test_file1, not cached)
# - README.md (not ignored, not cached)
# - test (subdirectory, not cached)
# - test_data (cached variable only)
test.df <- data.frame(
filename = c(test_file1, 'README.md', 'test', ''),
varname = c(gsub('.csv', '', test_file1), '', '', 'test_data'),
reader = c("csv.reader", "", "", ""),
is_ignored = c(FALSE, FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, TRUE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, TRUE),
cache_only = c(FALSE, FALSE, FALSE, TRUE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$varname, test.df$varname)
expect_equal(data.files$is_cached, test.df$is_cached)
expect_equal(data.files$cache_only, test.df$cache_only)
})
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context('List data')
temp_csv_file <- function(dir = '') {
gsub('^[/\\\\]', '', tempfile(pattern = "file", tmpdir = dir, fileext = ".csv"))
}
test_that('available data is listed correctly with default configuration', {
# Create temporary project
test_project <- tempfile('test_project')
suppressMessages(create.project(test_project))
on.exit(unlink(test_project, recursive = TRUE), add = TRUE)
# Set temporary project as working directory
oldwd <- setwd(test_project)
on.exit(setwd(oldwd), add = TRUE)
# Clear the global environment
clear()
# Create some test data so the file can be loaded if not ignored
test_data <- data.frame(Names = c("a", "b", "c"), Ages = c(20, 30, 40))
# Build two temporary filenames, strip leading /
test_file1 <- temp_csv_file()
test_file2 <- temp_csv_file(dir = 'test')
# Write test data to files
write.csv(test_data, file = file.path('data', test_file1), row.names = FALSE)
dir.create('data/test')
write.csv(test_data, file = file.path('data', test_file2), row.names = FALSE)
# Check if list.data can be called and returns a data.frame
expect_error(data.files <- list.data(), NA)
expect_true(is.data.frame(data.files))
# Check data.frame has a character variable "filename"
expect_true("filename" %in% names(data.files))
expect_true(class(data.files$filename) == "character")
# Check data.frame has a character variable "varname"
expect_true("varname" %in% names(data.files))
expect_true(class(data.files$varname) == "character")
# Check data.frame has a list variable "reader"
expect_true("reader" %in% names(data.files))
expect_true(class(data.files$reader) == "list")
# Check data.frame has a logical variable "is_ignored"
expect_true("is_ignored" %in% names(data.files))
expect_true(class(data.files$is_ignored) == "logical")
# Check data.frame has a logical variable "is_directory"
expect_true("is_directory" %in% names(data.files))
expect_true(class(data.files$is_directory) == "logical")
# Check data.frame has a logical variable "is_cached"
expect_true("is_cached" %in% names(data.files))
expect_true(class(data.files$is_cached) == "logical")
# Check data.frame has a logical variable "cache_only"
expect_true("cache_only" %in% names(data.files))
expect_true(class(data.files$cache_only) == "logical")
# Check if data.frame has three rows with default config:
# - fileXXXXX.csv (test_file1, not ignored, varname: fileXXXXX, reader: csv.reader)
# - README.md (not ignored, varname: "", reader: "")
# - test (subdirectory, not ignored, varname: "", reader: "")
expect_true(nrow(data.files) == 3)
test.df <- data.frame(
filename = c(test_file1, 'README.md', 'test'),
varname = c(gsub('.csv', '', test_file1), "", ""),
is_ignored = c(FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, TRUE),
is_cached = c(FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
test.df$reader <- list('csv.reader', '', '')
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$varname, test.df$varname)
expect_equal(data.files$reader, test.df$reader)
expect_equal(data.files$is_ignored, test.df$is_ignored)
expect_equal(data.files$is_directory, test.df$is_directory)
expect_equal(data.files$is_cached, test.df$is_cached)
expect_equal(data.files$cache_only, test.df$cache_only)
})
test_that('available data is listed correctly with recursive_loading = TRUE', {
# Create temporary project
test_project <- tempfile('test_project')
suppressMessages(create.project(test_project))
on.exit(unlink(test_project, recursive = TRUE), add = TRUE)
# Set temporary project as working directory
oldwd <- setwd(test_project)
on.exit(setwd(oldwd), add = TRUE)
# Read the config data and set cache_loaded_data to FALSE
config <- .read.config()
expect_error(config$recursive_loading <- TRUE, NA)
.save.config(config)
# Create some test data so the file can be loaded if not ignored
test_data <- data.frame(Names = c("a", "b", "c"), Ages = c(20, 30, 40))
# Build two temporary filenames, strip leading /
test_file1 <- temp_csv_file()
test_file2 <- temp_csv_file(dir = 'test')
# Write test data to files
write.csv(test_data, file = file.path('data', test_file1), row.names = FALSE)
dir.create('data/test')
write.csv(test_data, file = file.path('data', test_file2), row.names = FALSE)
# Setup test data.frame
test.df <- data.frame(
filename = c(test_file1, 'README.md', gsub("\\\\", "/", test_file2)),
varname = c(gsub('.csv', '', test_file1),
"",
gsub('[/\\\\]', '.', gsub('.csv', '', test_file2))),
is_ignored = c(FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, FALSE),
is_cached = c(FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
test.df$reader <- list("csv.reader", "", "csv.reader")
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
# Check if list.data can be called and returns a data.frame
expect_error(data.files <- list.data(), NA)
# Check if data.frame has three rows with default config:
# - fileXXXXX.csv (test_file1)
# - README.md
# - test/fileYYYYYY.csv (test_file2)
expect_true(nrow(data.files) == 3)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$varname, test.df$varname)
expect_equal(data.files$reader, test.df$reader)
expect_equal(data.files$is_directory, test.df$is_directory)
})
test_that('available data is listed correctly with data_ignore', {
# Create temporary project
test_project <- tempfile('test_project')
suppressMessages(create.project(test_project))
on.exit(unlink(test_project, recursive = TRUE), add = TRUE)
# Set temporary project as working directory
oldwd <- setwd(test_project)
on.exit(setwd(oldwd), add = TRUE)
# Create some test data so the file can be loaded if not ignored
test_data <- data.frame(Names = c("a", "b", "c"), Ages = c(20, 30, 40))
# Build two temporary filenames, strip leading /
test_file1 <- temp_csv_file()
test_file2 <- temp_csv_file(dir = 'test')
# Write test data to files
write.csv(test_data, file = file.path('data', test_file1), row.names = FALSE)
dir.create('data/test')
write.csv(test_data, file = file.path('data', test_file2), row.names = FALSE)
# Write an empty Thumbs.db that cannot be loaded by RSQLite
writeLines('\n', file.path('data', 'Thumbs.db'))
# Check if data.frame has four rows with default config:
# - fileXXXXX.csv (test_file1, not ignored)
# - README.md (not ignored)
# - test (subdirectory, not ignored)
# - Thumbs.db (ignored)
test.df <- data.frame(
filename = c(test_file1, 'README.md', 'test', 'Thumbs.db'),
varname = c(gsub('.csv', '', test_file1), "", "", ""),
reader = c("csv.reader", "", "", ""),
is_ignored = c(FALSE, FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, TRUE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_error(data.files <- list.data(), NA)
expect_true(nrow(data.files) == 4)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_ignored, test.df$is_ignored)
# Check empty data_ignore:
# - fileXXXXX.csv (test_file1, not ignored)
# - README.md (not ignored)
# - test/fileYYYYY.csv (test_file2, not ignored)
# - Thumbs.db (not ignored)
test.df <- data.frame(
filename = c(test_file1, 'README.md', gsub("\\\\", "/", test_file2), 'Thumbs.db'),
varname = c(gsub('.csv', '', test_file1),
"",
gsub('[/\\\\]', '.', gsub('.csv', '', test_file2)),
""),
reader = c("csv.reader", "", "csv.reader", ""),
is_ignored = c(FALSE, FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, FALSE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_error(data.files <- list.data(data_ignore = '',
recursive_loading = TRUE), NA)
expect_true(nrow(data.files) == 4)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_ignored, test.df$is_ignored)
# Check wildcard ignore "*.csv":
# - fileXXXXX.csv (test_file1, ignored)
# - README.md (not ignored)
# - test (subdirectory, not ignored)
# - Thumbs.db (not ignored)
test.df <- data.frame(
filename = c(test_file1, 'README.md', 'test', 'Thumbs.db'),
varname = c(gsub('.csv', '', test_file1), "", "", ""),
reader = c("csv.reader", "", "", ""),
is_ignored = c(TRUE, FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, TRUE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_error(data.files <- list.data(data_ignore = '*.csv'), NA)
expect_true(nrow(data.files) == 4)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_ignored, test.df$is_ignored)
# Check wildcard ignore "*.csv" with recursive loading on:
# - fileXXXXX.csv (test_file1, ignored)
# - README.md (not ignored)
# - test/fileYYYYY.csv (test_file2, not ignored)
# - Thumbs.db (not ignored)
test.df <- data.frame(
filename = c(test_file1, 'README.md', gsub("\\\\", "/", test_file2), 'Thumbs.db'),
varname = c(gsub('.csv', '', test_file1),
"",
gsub('[/\\\\]', '.', gsub('.csv', '', test_file2)),
""),
reader = c("csv.reader", "", "csv.reader", ""),
is_ignored = c(TRUE, FALSE, TRUE, FALSE),
is_directory = c(FALSE, FALSE, FALSE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_error(data.files <- list.data(data_ignore = '*.csv',
recursive_loading = TRUE), NA)
expect_true(nrow(data.files) == 4)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_ignored, test.df$is_ignored)
# Check regular expression ignore "^\w*.csv", only match csv in data, not in
# subdirectories:
# - fileXXXXX.csv (test_file1, ignored)
# - README.md (not ignored)
# - test/fileYYYYY.csv (test_file2, not ignored)
# - Thumbs.db (not ignored)
test.df <- data.frame(
filename = c(test_file1, 'README.md', gsub("\\\\", "/", test_file2), 'Thumbs.db'),
varname = c(gsub('.csv', '', test_file1),
"",
gsub('[/\\\\]', '.', gsub('.csv', '', test_file2)),
""),
reader = c("csv.reader", "", "csv.reader", ""),
is_ignored = c(TRUE, FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, FALSE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_error(data.files <- list.data(data_ignore = '/^\\w*\\.csv/',
recursive_loading = TRUE), NA)
expect_true(nrow(data.files) == 4)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_ignored, test.df$is_ignored)
# Check combination literal filename "Thumbs.db" and regular expression
# ignore "^\w*.csv", only match csv in data, not in subdirectories:
# - fileXXXXX.csv (test_file1, ignored)
# - README.md (not ignored)
# - test/fileYYYYY.csv (test_file2, not ignored)
# - Thumbs.db (ignored)
test.df <- data.frame(
filename = c(test_file1, 'README.md', gsub("\\\\", "/", test_file2), 'Thumbs.db'),
varname = c(gsub('.csv', '', test_file1),
"",
gsub('[/\\\\]', '.', gsub('.csv', '', test_file2)),
""),
reader = c("csv.reader", "", "csv.reader", ""),
is_ignored = c(TRUE, FALSE, FALSE, TRUE),
is_directory = c(FALSE, FALSE, FALSE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_error(data.files <- list.data(data_ignore = 'Thumbs.db, /^\\w*\\.csv/',
recursive_loading = TRUE), NA)
expect_true(nrow(data.files) == 4)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_ignored, test.df$is_ignored)
# Check extra comma in combination literal filename "Thumbs.db" and regular
# expression ignore "^\w*\.csv", only match csv in data, not in
# subdirectories:
# - fileXXXXX.csv (test_file1, ignored)
# - README.md (not ignored)
# - test/fileYYYYY.csv (test_file2, not ignored)
# - Thumbs.db (ignored)
test.df <- data.frame(
filename = c(test_file1, 'README.md', gsub("\\\\", "/", test_file2), 'Thumbs.db'),
varname = c(gsub('.csv', '', test_file1),
"",
gsub('[/\\\\]', '.', gsub('.csv', '', test_file2)),
""),
reader = c("csv.reader", "", "csv.reader", ""),
is_ignored = c(TRUE, FALSE, FALSE, TRUE),
is_directory = c(FALSE, FALSE, FALSE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_error(data.files <- list.data(data_ignore = 'Thumbs.db,,/^\\w*\\.csv/',
recursive_loading = TRUE), NA)
expect_true(nrow(data.files) == 4)
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_ignored, test.df$is_ignored)
})
test_that('cached data is listed correctly as already cached', {
# Create temporary project
test_project <- tempfile('test_project')
suppressMessages(create.project(test_project))
on.exit(unlink(test_project, recursive = TRUE), add = TRUE)
# Set temporary project as working directory
oldwd <- setwd(test_project)
on.exit(setwd(oldwd), add = TRUE)
# Clear the global environment
clear()
# Create some test data so the file can be loaded if not ignored
test_data <- data.frame(Names = c("a", "b", "c"), Ages = c(20, 30, 40))
# Build two temporary filenames
test_file1 <- temp_csv_file()
test_file2 <- temp_csv_file(dir = 'test')
# Write test data to files
write.csv(test_data, file = file.path('data', test_file1), row.names = FALSE)
dir.create('data/test')
write.csv(test_data, file = file.path('data', test_file2), row.names = FALSE)
expect_error(data.files <- list.data(), NA)
# Check if data.frame has three rows with default config:
# - fileXXXXX.csv (test_file1, not cached)
# - README.md (not ignored, not cached)
# - test (subdirectory, not cached)
test.df <- data.frame(
filename = c(test_file1, 'README.md', 'test'),
varname = c(gsub('.csv', '', test_file1), '', ''),
reader = c("csv.reader", "", ""),
is_ignored = c(FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, TRUE),
is_cached = c(FALSE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_cached, test.df$is_cached)
# Load the project so variables are cached, then list data again
suppressMessages(load.project())
expect_error(data.files <- list.data(), NA)
# Check if data.frame has three rows with default config:
# - fileXXXXX.csv (test_file1, cached)
# - README.md (not ignored, not cached)
# - test (subdirectory, not cached)
test.df <- data.frame(
filename = c(test_file1, 'README.md', 'test'),
varname = c(gsub('.csv', '', test_file1), '', ''),
reader = c("csv.reader", "", ""),
is_ignored = c(FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, TRUE),
is_cached = c(TRUE, FALSE, FALSE),
cache_only = c(FALSE, FALSE, FALSE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$is_cached, test.df$is_cached)
})
test_that('cached data created during munging listed as cached only', {
skip_if_not_installed("formatR")
# Create temporary project
test_project <- tempfile('test_project')
suppressMessages(create.project(test_project))
on.exit(unlink(test_project, recursive = TRUE), add = TRUE)
# Set temporary project as working directory
oldwd <- setwd(test_project)
on.exit(setwd(oldwd), add = TRUE)
# Clear the global environment
clear()
# Create some test data so the file can be loaded if not ignored
test_data <- data.frame(Names = c("a", "b", "c"), Ages = c(20, 30, 40))
# Build two temporary filenames
test_file1 <- temp_csv_file()
test_file2 <- temp_csv_file(dir = 'test')
# Write test data to files
write.csv(test_data, file = file.path('data', test_file1), row.names = FALSE)
dir.create('data/test')
write.csv(test_data, file = file.path('data', test_file2), row.names = FALSE)
# Cache a code fragment
cache(variable = "test_data", CODE = {
data.frame(Names = c("a", "b", "c"), Ages = c(20, 30, 40))
})
expect_error(data.files <- list.data(), NA)
# Check if data.frame has four rows with default config:
# - fileXXXXX.csv (test_file1, not cached)
# - README.md (not ignored, not cached)
# - test (subdirectory, not cached)
# - test_data (cached variable only)
test.df <- data.frame(
filename = c(test_file1, 'README.md', 'test', ''),
varname = c(gsub('.csv', '', test_file1), '', '', 'test_data'),
reader = c("csv.reader", "", "", ""),
is_ignored = c(FALSE, FALSE, FALSE, FALSE),
is_directory = c(FALSE, FALSE, TRUE, FALSE),
is_cached = c(FALSE, FALSE, FALSE, TRUE),
cache_only = c(FALSE, FALSE, FALSE, TRUE),
stringsAsFactors = FALSE
)
# Sort data.frame according to collation of the testing process (for example
# LC_COLLATE=C and LC_COLLATE=en_US.UTF-8 return different order)
sort.df <- order(test.df$cache_only, test.df$filename, test.df$varname)
test.df <- test.df[sort.df,]
expect_equal(data.files$filename, test.df$filename)
expect_equal(data.files$varname, test.df$varname)
expect_equal(data.files$is_cached, test.df$is_cached)
expect_equal(data.files$cache_only, test.df$cache_only)
})
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