Nothing
tests/testthat/test_render_clinDataReviewReport.R
In clinDataReview: Clinical Data Review Tool
context("Render a clinical data review report")
library(yaml)
library(parallel)
library(xml2)
test_that("Report titles are extracted for each config file", {
# get example config files
testPathConfig <- normalizePath(file.path("../files", "config"))
configFiles <- list.files(testPathConfig)
otherConfigs <- configFiles[!grepl("config.yml", configFiles)]
reportTitles <- clinDataReview:::checkReportTitles(configFiles, configDir = testPathConfig)
expect_type(reportTitles, "character")
expect_length(reportTitles, length(otherConfigs))
expect_named(reportTitles, otherConfigs)
})
test_that("An error is generated if the multiple reports have the same titles", {
# get example config files
testPathConfig <- normalizePath(file.path("../files", "config"))
configFiles <- list.files(testPathConfig)
configFilesError <- c(configFiles[1], configFiles[1])
expect_error(
clinDataReview:::checkReportTitles(configFilesError, configDir = testPathConfig),
"The title .+ is duplicated."
)
})
test_that("A warning is generated if a config is generated if a config file doesn't exist", {
# get example config files
testPathConfig <- normalizePath(file.path("../files", "config"))
configFiles <- list.files(testPathConfig)
configFilesWarning <- c(configFiles, "config-ciao")
expect_warning(
clinDataReview:::checkReportTitles(configFilesWarning, configDir = testPathConfig),
"Please check the spelling is correct"
)
})
test_that("Paths of markdown files are extracted correctly from the config files", {
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
configFiles <- list.files(testPathConfig)
testPathInterim <- file.path(testPathBase, "interim")
otherConfigs <- configFiles[!grepl("config.yml", configFiles)]
mdFiles <- clinDataReview:::getMdFromConfig(configFiles, intermediateDir = testPathInterim)
expect_type(mdFiles, "character")
expect_length(mdFiles, length(configFiles))
mdNames <- file.path(
testPathInterim,
c(
gsub("config-(.+).yml", "\\1.md", otherConfigs),
"index.md"
))
expect_identical(object = mdNames, expected = mdFiles)
})
test_that("Names of markdown files are extracted correctly from the config files when a custom index file is specified", {
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
configFiles <- list.files(testPathConfig)
otherConfigs <- configFiles[!grepl("config.yml", configFiles)]
testPathInterim <- file.path(testPathBase, "interim")
# Different name for indexPath
mdFilesIndex <- clinDataReview:::getMdFromConfig(
configFiles,
indexPath = "myIndex.Rmd",
intermediateDir = testPathInterim
)
expect_type(mdFilesIndex, "character")
expect_length(object = mdFilesIndex, n = length(configFiles))
mdNames <- file.path(
testPathInterim,
c(
gsub("config-(.+).yml", "\\1.md", otherConfigs),
"myIndex.md"
)
)
expect_identical(object = mdNames, expected = mdFilesIndex)
})
test_that("Names of markdown files are extracted correctly from the config files when a custom intermediate directory is specified", {
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
configFiles <- list.files(testPathConfig)
otherConfigs <- configFiles[!grepl("config.yml", configFiles)]
mdFilesInterim <- clinDataReview:::getMdFromConfig(configFiles, intermediateDir = "myDir")
expect_type(mdFilesInterim, "character")
expect_length(mdFilesInterim, length(configFiles))
mdNames <- file.path("myDir", c(
gsub("config-(.+).yml", "\\1.md", otherConfigs),
"index.md"
))
expect_identical(object = mdNames, expected = mdFilesInterim)
})
test_that("Parameters are extracted correctly from a general config file", {
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
listConfig <- getParamsFromConfig("config.yml", configDir = testPathConfig)
filePathGeneralConfig <- file.path(testPathConfig, "config.yml")
configFromYaml <- read_yaml(filePathGeneralConfig)
expect_type(listConfig, "list")
expect_length(configFromYaml, length(listConfig))
expect_identical(
object = listConfig,
expected = configFromYaml
)
})
test_that("Parameters are extracted correctly from a chapter-specific config file", {
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
listConfig <- getParamsFromConfig("config-adverseEvents-division.yml", configDir = testPathConfig)
configFromYamlGeneral <- read_yaml(file.path(testPathConfig, "config.yml"))
configFromYaml <- read_yaml(file.path(testPathConfig, "config-adverseEvents-division.yml"))
expect_type(listConfig, "list")
expect_length(
object = listConfig,
n = length(configFromYamlGeneral) + length(configFromYaml)
)
expect_mapequal(
object = listConfig,
expected = c(configFromYamlGeneral, configFromYaml)
)
})
test_that("An error is generated if the config directory is not available", {
configDir <- tempfile(pattern = "config")
expect_error(
getParamsFromConfig(configFile = "config.yml", configDir = configDir),
"Config directory: .+ doesn't exist."
)
})
test_that("An error is generated if a config file is not available", {
configDir <- tempfile(pattern = "config")
dir.create(configDir)
# get example general config file
testPathConfig <- normalizePath(file.path("../files", "config"))
file.copy(from = file.path(testPathConfig, "config.yml"), to = configDir)
expect_error(
getParamsFromConfig(configFile = "config-test.yml", configDir = configDir),
"File .+ cannot be found."
)
})
test_that("A warning is generated if the general config file is not available", {
configFileTemp <- tempfile(pattern = "config-", fileext = ".yml")
write_yaml(list(), configFileTemp)
expect_warning(
output <- getParamsFromConfig(
configFile = basename(configFileTemp),
configDir = dirname(configFileTemp)
),
"General config file: .+ not available"
)
expect_type(output, "list")
})
test_that("The creation of html file from the specified markdown files is successful", {
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
testPathInterim <- file.path(testPathBase, "interim")
# copy md file to temp directory
testDir <- tempfile("mdConversion")
dir.create(testDir)
tmp <- file.copy(from = testPathInterim, to = testDir, recursive = TRUE)
interimDir <- file.path(testDir, basename(testPathInterim))
# Md files
filePathMd <- file.path(interimDir, "adverseEvents-division.md")
expect_message(
htmlOutput <- clinDataReview:::convertMdToHtml(
mdFile = filePathMd,
indexPath = file.path(testPathBase, "index.Rmd"),
intermediateDir = interimDir,
outputDir = interimDir,
quiet = TRUE, # suppress printing of pandoc cmd line
),
"Convert the Markdown file.+to html.+"
)
expect_type(htmlOutput, "character")
expect_true(file.exists(htmlOutput))
expect_equal(normalizePath(dirname(htmlOutput)), normalizePath(interimDir))
})
test_that("The template name is successfully checked from correct config files", {
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
configFiles <- list.files(testPathConfig)
expect_silent(
checkedConfig <- clinDataReview:::checkTemplatesName(
configFiles = configFiles, configDir = testPathConfig
)
)
expect_type(checkedConfig, "character")
expect_identical(object = checkedConfig, expected = configFiles)
})
test_that("A warning is generated if a config file has no template name", {
testDir <- tempfile("config-templateName")
dir.create(testDir)
# create a general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(x = list(), file = configFileGeneral)
configFileTemplate <- tempfile(
pattern = "config-test", fileext = ".yml",
tmpdir = testDir
)
write_yaml(
x = list(reportTitle = "Title", reportTitleLevel = 2),
file = configFileTemplate
)
expect_warning(
clinDataReview:::checkTemplatesName(
configFiles = basename(configFileTemplate),
configDir = testDir
),
"Import of parameters from config file .+ failed with error:"
)
})
test_that("A warning is generated if config files with the same template name in different packages are used", {
testDir <- tempfile("config-sameTemplateName")
dir.create(testDir)
# create a general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(x = list(), file = configFileGeneral)
# create a first config file
configFileTemplate <- tempfile(pattern = "config-", fileext = ".yml", tmpdir = testDir)
write_yaml(
x = list(reportTitle = "Title", reportTitleLevel = 2,
template = "divisionTemplate", templatePackage = "custom"
),
file = configFileTemplate
)
configFileTemplate <- basename(configFileTemplate)
# create a second config file
configFileTemplateBis <- tempfile(pattern = "config-", fileext = ".yml", tmpdir = testDir)
write_yaml(
x = list(reportTitle = "Title", reportTitleLevel = 2,
template = "divisionTemplate", templatePackage = "clinDataReview"
),
file = configFileTemplateBis
)
configFileTemplateBis <- basename(configFileTemplateBis)
# check templates
configFileTemplates <- basename(c(configFileTemplate, configFileTemplateBis))
expect_warning(
output <- clinDataReview:::checkTemplatesName(
configFiles = configFileTemplates,
configDir = testDir
),
"The following config file.* are ignored, because the same template name is used"
)
expect_length(output, 0)
})
test_that("Session informations are merged successfully", {
sessionInfos <- list(sessionInfo(), sessionInfo())
sessionInfo <- do.call(clinDataReview:::merge.sessionInfo, sessionInfos)
expect_s3_class(sessionInfo, "sessionInfo")
})
test_that("Session informations with different elements are merged successfully", {
sessionInfos <- list(sessionInfo(), sessionInfo())
sessionInfos[[1]]$loadedOnly <- NULL
expect_silent(
sessionInfo <- do.call(clinDataReview:::merge.sessionInfo, sessionInfos)
)
expect_s3_class(sessionInfo, "sessionInfo")
})
test_that("The export of empty session infos to Markdown returns an empty output", {
expect_null(clinDataReview:::exportSessionInfoToMd(sessionInfos = NULL))
})
test_that("Session infos are successfully exported to Markdown", {
interimDir <- tempfile("interim")
sessionInfos <- list(sessionInfo(), sessionInfo())
mdFile <- clinDataReview:::exportSessionInfoToMd(
sessionInfos = sessionInfos,
intermediateDir = interimDir,
quiet = TRUE # suppress printing of pandoc cmd line
)
expect_type(mdFile, "character")
expect_true(file.exists(mdFile))
expect_identical(mdFile, file.path(interimDir, "sessionInfo.md"))
})
test_that("A clinical data report is created successfully via the specification of config files", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
configFiles <- list.files(testPathConfig)
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
outputDir <- file.path(testDir, "report")
# copy index file
file.copy(from = indexPath, to = testDir)
# copy configuration files
file.copy(from = testPathConfig, to = testDir, recursive = TRUE)
output <- render_clinDataReviewReport(
configFiles = configFiles,
configDir = testPathConfig,
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = outputDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
)
expect_type(output, "character")
expect_match(output, "introduction")
htmlFiles <- list.files(pattern = "html", outputDir)
expect_true(
any(grepl("1-introduction", htmlFiles))
)
})
test_that("A clinical data report is created successfully with a log file", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
# copy index file
file.copy(from = indexPath, to = testDir)
# copy configuration files
file.copy(from = testPathConfig, to = testDir, recursive = TRUE)
logPath <- file.path(testDir, "log.txt")
output <- render_clinDataReviewReport(
configDir = testPathConfig,
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = file.path(testDir, "report"),
logFile = logPath
)
expect_type(output, "character")
expect_match(output, "introduction")
expect_true(file.exists(logPath))
})
test_that("A clinical data report is created successfully via the specification of a config directory", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
configFiles <- list.files(testPathConfig)
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
outputDir <- file.path(testDir, "report")
# copy index file
file.copy(from = indexPath, to = testDir)
# copy configuration files
file.copy(from = testPathConfig, to = testDir, recursive = TRUE)
output <- render_clinDataReviewReport(
configFiles = NULL,
configDir = file.path(testDir, basename(testPathConfig)),
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = outputDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
)
expect_type(output, "character")
expect_match(output, "introduction")
htmlFiles <- list.files(pattern = "html", path = outputDir)
sectionName <- clinDataReview:::checkReportTitles(configFiles, configDir = testPathConfig)
sectionName <- gsub(" ", "-", sectionName)
expect_true(
any(grepl(sectionName, htmlFiles, ignore.case = TRUE))
)
})
test_that("A warning is generated if a specified config file doesn't exist", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
# copy index file
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
template = "divisionTemplate.Rmd",
templatePackage = "clinDataReview",
reportTitle = "Adverse events",
reportTitleLevel = 1
),
file = configFile1
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(
basename(configFile1),
"configFile2.yml"
)
),
file = configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1, "configFile2.yml")
configFiles <- basename(configFiles)
expect_warning(
output <- render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
inputDir = testDir,
intermediateDir = testDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
"configFile2.* cannot be found"
)
expect_type(output, "character")
expect_match(output, "introduction")
})
test_that("A warning is generated if a template report is already available", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
template = "divisionTemplate.Rmd",
templatePackage = "clinDataReview",
reportTitle = "Adverse events",
reportTitleLevel = 1
),
file = configFile1
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(
basename(configFile1)
)
),
file = configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1)
configFiles <- basename(configFiles)
# progress messages during execution
firstRun <- render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
inputDir = testDir,
intermediateDir = testDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
)
expect_warning(
secondRun <- render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
inputDir = testDir,
intermediateDir = testDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
"Document with similar name than specified template from"
)
expect_type(secondRun, "character")
expect_match(secondRun, regexp = "introduction")
})
test_that("A warning is generated if the creation of a chapter fails'", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
template = "templateWithError.Rmd",
sectionTitle = "Chapter with error"
),
file = configFile1
)
# create a Rmd file returning an error
cat(
"```{r}",
"stop('test')",
"```",
file = file.path(testDir, "templateWithError.Rmd"),
sep = "\n"
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(basename(configFile1))
),
file = configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1)
configFiles <- basename(configFiles)
expect_warning(
render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
intermediateDir = testDir,
inputDir = testDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
paste(
"Rendering of the .+ report for config file:.+configFile1.yml.+failed,",
"a report with only the section title is created.+")
)
})
test_that("A warning is generated if the template name is missing in a config file", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
reportTitle = "Adverse events",
reportTitleLevel = 1
),
file = configFile1
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(basename(configFile1))
),
file = configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1)
configFiles <- basename(configFiles)
expect_warning(
res <- render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
intermediateDir = testDir,
inputDir = testDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
"Template missing for config file: .+."
)
expect_type(res, "character")
expect_match(object = res, regexp = "introduction")
})
test_that("A warning is generated if the config parameters don't comply to the template specifications", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
template = "divisionTemplate.Rmd",
templatePackage = "clinDataReview"
),
file = configFile1
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(basename(configFile1))
),
file = configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1)
configFiles <- basename(configFiles)
expect_warning(
res <- render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
intermediateDir = testDir,
inputDir = testDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
"The report for the config file: .+ is not created because the check of the parameters failed"
)
expect_type(res, "character")
expect_match(object = res, regexp = "introduction")
})
test_that("A warning is generated if a template is not available in the specified package", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
template = "divisionTemplate.Rmd",
templatePackage = "myPackage"
),
file = configFile1
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(basename(configFile1))
),
file = configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1)
configFiles <- basename(configFiles)
expect_warning(
res <- render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
intermediateDir = testDir,
inputDir = testDir ,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
"Template file: .+ not available in.*myPackage.+ package."
)
expect_type(res, "character")
expect_match(object = res, regexp = "introduction")
})
test_that("A warning is generated if no config parameters are available", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
template = "subjectProfile.Rnw",
templatePackage = "patientProfilesVis"
),
file = configFile1
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(basename(configFile1))
),
configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1)
configFiles <- basename(configFiles)
expect_warning(
res <- render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
intermediateDir = testDir,
inputDir = testDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
"No config parameter available, input parameters for the report are not checked."
)
})
test_that("A warning is generated if some Markdown files are missing for conversion to html", {
testDir <- tempfile("report")
dir.create(testDir)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
template = "divisionTemplate.Rmd",
templatePackage = "myPackage"
),
file = configFile1
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(basename(configFile1))
),
file = configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1)
configFiles <- basename(configFiles)
expect_error(
expect_warning(
postProcessReport(
configDir = testDir,
outputDir = testDir,
intermediateDir = testDir,
inputDir = testDir,
mdFiles = NULL,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
"Markdown file(s): .+ are missing, these files are ignored."
)
)
})
test_that("Config parameters with R code are correctly evaluated", {
configDir <- tempfile("config-r-eval")
dir.create(configDir)
# get example general config file
testPathConfig <- normalizePath(file.path("../files", "config"))
file.copy(from = file.path(testPathConfig, "config.yml"), to = configDir)
configFileTemp <- tempfile(pattern = "config-", fileext = ".yml", tmpdir = configDir)
write_yaml(list(param = structure("toString(c('a', 'b'))", tag = "!r")), configFileTemp)
# parameter is replaced by its evaluated version:
params <- getParamsFromConfig(
configFile = basename(configFileTemp),
configDir = configDir
)
expect_equal(params$param, "a, b")
})
test_that("Config parameters with R code and lazy-evaluation are imported non evaluated", {
configDir <- tempfile("config-r-eval-lazy")
dir.create(configDir)
# get example general config file
testPathConfig <- normalizePath(file.path("../files", "config"))
file.copy(from = file.path(testPathConfig, "config.yml"), to = configDir)
configFileTemp <- tempfile(pattern = "config-", fileext = ".yml", tmpdir = configDir)
write_yaml(list(param = structure("nrow(dataI)", tag = "!r-lazy")), configFileTemp)
params <- getParamsFromConfig(
configFile = basename(configFileTemp),
configDir = configDir
)
expect_type(params, "list")
expect_s3_class(params[["param"]], c("r-lazy", "character"))
expect_equal(as.character(params[["param"]]), "nrow(dataI)")
})
test_that("An error is generated if the R code specified in config parameters with lazy-evaluation contains errors", {
params <- list(nrowData = structure("nrow(customData)", class = "r-lazy"))
# error if R object is missing
expect_error(
forceParams(params),
".*customData.* not found"
)
})
test_that("Config parameters with R code and lazy-evaluation are correctly evaluated when requested", {
params <- list(nrowData = structure("nrow(customData)", class = "r-lazy"))
# parameter is replaced by its evaluated version:
customData <- data.frame(A = seq.int(2), B = c("A", "B"))
expect_silent(paramEvaluated <- forceParams(params))
expect_type(paramEvaluated, "list")
expect_named(paramEvaluated, "nrowData")
expect_equal(paramEvaluated$nrowData, nrow(customData))
})
test_that("A clinical data report is created successfully in parallel", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
testDir <- tempfile("report")
dir.create(testDir)
# create multiple config files
configDir <- file.path(testDir, "config")
dir.create(configDir)
nChapters <- 4
configFiles <- file.path(configDir,
paste0("config-division-", seq_len(nChapters), ".yml")
)
for(i in seq_len(nChapters)){
yaml::write_yaml(
list(
template = "divisionTemplate.Rmd",
templatePackage = "clinDataReview",
reportTitle = paste("Chapter", i),
reportTitleLevel = 1
),
configFiles[i]
)
}
# create general config file
yaml::write_yaml(
x = list(config = as.list(basename(configFiles))),
file = file.path(configDir, "config.yml")
)
# example index file
indexPath <- file.path(testDir, "index.Rmd")
cat(
"---",
"title: 'Clinical data report'",
"output: clinDataReview::gitbook_clinDataReview_report",
"---",
"# Introduction",
file = indexPath, sep = "\n"
)
outputDir <- file.path(testDir, "report")
output <- render_clinDataReviewReport(
configDir = configDir,
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = outputDir,
nCores = min(parallel::detectCores(), 2),
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
)
# check that all filenames are correct
htmlFiles <- list.files(pattern = ".html$", outputDir)
htmlFiles <- setdiff(htmlFiles, "404.html")
htmlFilesExp <- c(
"1-introduction.html",
paste0(2:5, "-chapter-", 1:4, ".html"),
"6-appendix.html"
)
expect_setequal(object = htmlFiles, expected = htmlFilesExp)
})
test_that("A clinical data report is created successfully in parallel with one chapter containing parallel execution", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
testDir <- tempfile("report")
dir.create(testDir)
configDir <- file.path(testDir, "config")
dir.create(configDir)
# create multiple config files
nChapters <- 4
configFiles <- file.path(configDir,
paste0("config-division-", seq_len(nChapters), ".yml")
)
for(i in seq_len(nChapters)){
yaml::write_yaml(
x = list(
template = "divisionTemplate.Rmd",
templatePackage = "clinDataReview",
reportTitle = paste("Chapter", i),
reportTitleLevel = 1
),
file = configFiles[i]
)
}
# create example chapter run in parallel
chapterParallel <- file.path(testDir, "chapter-parallel.Rmd")
cat(
"# Parallel",
"```{r eval = TRUE, echo = FALSE, class.output = \"testParallel\", comment = NA}",
"library(parallel)",
"cl <- makeCluster(2)",
"print(clusterApply(cl, 1:2, get('+'), 3))",
"stopCluster(cl = cl)",
"```",
file = chapterParallel, sep = "\n"
)
configFileParallel <- file.path(configDir, "config-parallel.yml")
yaml::write_yaml(
x = list(
template = basename(chapterParallel),
parallel = TRUE
),
file = configFileParallel
)
configFiles <- c(configFiles, configFileParallel)
# create general config file
yaml::write_yaml(
x = list(config = as.list(basename(configFiles))),
file = file.path(configDir, "config.yml")
)
# example index file
indexPath <- file.path(testDir, "index.Rmd")
cat(
"---",
"title: 'Clinical data report'",
"output: clinDataReview::gitbook_clinDataReview_report",
"---",
"# Introduction",
file = indexPath, sep = "\n"
)
# progress messages during execution
outputDir <- file.path(testDir, "report")
expect_error(
output <- render_clinDataReviewReport(
configDir = configDir,
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = outputDir,
nCores = min(parallel::detectCores(), 2),
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
NA
)
# check that all filenames are correct
htmlFiles <- list.files(pattern = "html", outputDir)
htmlFiles <- setdiff(htmlFiles, "404.html")
htmlFilesExp <- c(
"1-introduction.html",
paste0(2:5, "-chapter-", 1:4, ".html"),
"6-parallel.html",
"7-appendix.html"
)
expect_setequal(object = htmlFiles, expected = htmlFilesExp)
# check the content of the chapter run in parallel
htmlFileParallel <- xml2::read_xml(x = file.path(outputDir, "6-parallel.html"))
headXML <- xml2::xml_find_all(x = htmlFileParallel, xpath = ".//h1[span]")
expect_equal(object = xml2::xml_text(headXML), expected = "6 Parallel")
codeXML <- xml2::xml_find_all(
x = htmlFileParallel,
xpath = ".//pre[contains(@class, 'testParallel')]//code"
)
expect_match(object = xml2::xml_text(codeXML), regexp = "4.+5")
})
test_that("A report is correctly split at different chapter-specific levels", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
testDir <- tempfile("report")
dir.create(testDir)
# create multiple config files + template
template <- file.path(testDir, "chapter.Rmd")
cat(
"# Chapter",
"## Section 1",
"### Subsection 1",
"### Subsection 2",
"## Section 2",
file = template, sep = "\n"
)
configDir <- file.path(testDir, "config")
dir.create(configDir)
configFiles <- file.path(configDir,
paste0("config-division-", c("chapter", "section", "subsection"), ".yml")
)
for(i in seq_along(configFiles)){
yaml::write_yaml(
x = list(
template = basename(template),
split_by = as.integer(i),
reportTitle = paste("Chapter split at level", i)
),
file = configFiles[i]
)
}
# create general config file
yaml::write_yaml(
x = list(config = as.list(basename(configFiles))),
file = file.path(configDir, "config.yml")
)
# example index file
indexPath <- file.path(testDir, "index.Rmd")
cat(
"---",
"title: 'Clinical data report'",
"output:",
" clinDataReview::gitbook_clinDataReview_report:",
" split_by: 'section+number'",
"---",
"# Introduction",
file = indexPath, sep = "\n"
)
# progress messages during execution
outputDir <- file.path(testDir, "report")
output <- render_clinDataReviewReport(
configDir = configDir,
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = outputDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
)
expect_type(output, "character")
expect_match(output, "introduction")
# check that all filenames are correct
htmlFiles <- list.files(pattern = "html", outputDir)
htmlFiles <- setdiff(htmlFiles, "404.html")
htmlFilesExp <- c(
"1-introduction.html",
# split at chapter level
"2-chapter.html",
# split at the section level
"3-chapter.html",
"3.1-section-1.html", "3.2-section-2.html",
# split at the subsection level
"4-chapter.html",
"4.1-section-1.html", "4.1.1-subsection-1.html",
"4.1.2-subsection-2.html", "4.2-section-2.html",
"5-appendix.html",
"5.1-session-information.html"
)
expect_setequal(object = htmlFiles, expected = htmlFilesExp)
# check if content is correct
getHeaders <- function(file){
x <- xml2::read_xml(x = file)
headXML <- xml2::xml_find_all(x = x, xpath = ".//h1[span]|.//h2[span]|.//h3[span]")
headers <- xml2::xml_text(headXML)
return(headers)
}
# split at the chapter level
expect_setequal(
object = getHeaders(file = file.path(outputDir, "2-chapter.html")),
expected = c("2 Chapter", "2.1 Section 1", "2.1.1 Subsection 1",
"2.1.2 Subsection 2", "2.2 Section 2")
)
# split at the section level
expect_setequal(
object = getHeaders(file = file.path(outputDir, "3-chapter.html")),
expected = "3 Chapter"
)
expect_setequal(
object = getHeaders(file = file.path(outputDir, "3.1-section-1.html")),
expected = c("3.1 Section 1", "3.1.1 Subsection 1", "3.1.2 Subsection 2")
)
expect_setequal(
object = getHeaders(file = file.path(outputDir, "3.2-section-2.html")),
expected = "3.2 Section 2"
)
# split at the subsection level
expect_setequal(
object = getHeaders(file = file.path(outputDir, "4-chapter.html")),
expected = "4 Chapter"
)
expect_setequal(
object = getHeaders(file = file.path(outputDir, "4.1-section-1.html")),
expected = "4.1 Section 1"
)
expect_setequal(
object = getHeaders(file = file.path(outputDir, "4.1.1-subsection-1.html")),
expected = "4.1.1 Subsection 1"
)
expect_setequal(
object = getHeaders(file = file.path(outputDir, "4.1.2-subsection-2.html")),
expected = "4.1.2 Subsection 2"
)
expect_setequal(
object = getHeaders(file = file.path(outputDir, "4.2-section-2.html")),
expected = "4.2 Section 2"
)
})
test_that("The page titles are correctly set for a report", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
testDir <- tempfile("report")
dir.create(testDir)
# create multiple config files + template
template <- file.path(testDir, "chapter.Rmd")
cat(
"# Chapter",
"## Section 1",
"### Subsection 1",
"### Subsection 2",
"## Section 2",
file = template, sep = "\n"
)
configDir <- file.path(testDir, "config")
dir.create(configDir)
configFiles <- file.path(configDir,
paste0("config-division-", c("chapter", "section", "subsection"), ".yml")
)
for(i in seq_along(configFiles)){
yaml::write_yaml(
x = list(
template = basename(template),
split_by = as.integer(i),
reportTitle = paste("Chapter split at level", i)
),
file = configFiles[i]
)
}
# create general config file
yaml::write_yaml(
x = list(config = as.list(basename(configFiles))),
file = file.path(configDir, "config.yml")
)
# example index file
indexPath <- file.path(testDir, "index.Rmd")
cat(
"---",
"title: 'Clinical data report'",
"output:",
" clinDataReview::gitbook_clinDataReview_report:",
" split_by: 'section+number'",
"---",
"# Introduction",
file = indexPath, sep = "\n"
)
# progress messages during execution
outputDir <- file.path(testDir, "report")
output <- render_clinDataReviewReport(
configDir = configDir,
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = outputDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
)
getTitle <- function(file){
x <- xml2::read_xml(x = file)
titleXML <- xml2::xml_find_all(x = x, xpath = ".//title")
titles <- xml2::xml_text(titleXML)
return(titles)
}
# split at the chapter level
expect_equal(
object = getTitle(file = file.path(outputDir, "2-chapter.html")),
expected = "2 Chapter | Clinical data report"
)
# split at the section level
expect_equal(
object = getTitle(file = file.path(outputDir, "3-chapter.html")),
expected = "3 Chapter | Clinical data report"
)
expect_equal(
object = getTitle(file = file.path(outputDir, "3.1-section-1.html")),
expected = "3.1 Section 1 | Clinical data report"
)
expect_equal(
object = getTitle(file = file.path(outputDir, "3.2-section-2.html")),
expected = "3.2 Section 2 | Clinical data report"
)
# split at the subsection level
expect_setequal(
object = getTitle(file = file.path(outputDir, "4-chapter.html")),
expected = "4 Chapter | Clinical data report"
)
expect_equal(
object = getTitle(file = file.path(outputDir, "4.1-section-1.html")),
expected = "4.1 Section 1 | Clinical data report"
)
expect_equal(
object = getTitle(file = file.path(outputDir, "4.1.1-subsection-1.html")),
expected = "4.1.1 Subsection 1 | Clinical data report"
)
expect_equal(
object = getTitle(file = file.path(outputDir, "4.1.2-subsection-2.html")),
expected = "4.1.2 Subsection 2 | Clinical data report"
)
expect_equal(
object = getTitle(file = file.path(outputDir, "4.2-section-2.html")),
expected = "4.2 Section 2 | Clinical data report"
)
})
test_that("The table of contents is correctly set for a report", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
testDir <- tempfile("report")
dir.create(testDir)
# create multiple config files + template
template <- file.path(testDir, "chapter.Rmd")
cat(
"# Chapter",
"## Section 1",
"## Section 2",
"### Subsection 1",
"### Subsection 2", # to test difference of level > 1 with next chapter
file = template, sep = "\n"
)
configDir <- file.path(testDir, "config")
dir.create(configDir)
configFiles <- file.path(configDir,
paste0("config-division-", c("chapter", "section"), ".yml")
)
for(i in seq_along(configFiles)){
yaml::write_yaml(
x = list(
template = basename(template),
split_by = as.integer(i),
reportTitle = paste("Chapter split at level", i)
),
file = configFiles[i]
)
}
# create general config file
yaml::write_yaml(
x = list(config = as.list(basename(configFiles))),
file = file.path(configDir, "config.yml")
)
# example index file
indexPath <- file.path(testDir, "index.Rmd")
cat(
"---",
"title: 'Clinical data report'",
"output:",
" clinDataReview::gitbook_clinDataReview_report:",
" split_by: 'section+number'",
"---",
"# Introduction",
file = indexPath, sep = "\n"
)
# progress messages during execution
outputDir <- file.path(testDir, "report")
output <- render_clinDataReviewReport(
configDir = configDir,
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = outputDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
)
# import introduction and table of contents
book <- read_html(x = file.path(outputDir, "1-introduction.html"))
toc <- xml_find_all(book, ".//ul[@class='summary']")
checkHeader <- function(x, title, link){
head <- xml2::xml_find_first(x, ".//a")
expect_equal(object = xml2::xml_text(head), expected = title)
expect_equal(object = xml2::xml_attr(head, "href"), expected = link)
}
getSublist <- function(x){
xml_children(xml2::xml_find_first(x, ".//ul"))
}
tocChapters <- xml2::xml_children(toc)
# intro
checkHeader(
x = tocChapters[[1]],
title = "1 Introduction",
link = "1-introduction.html#introduction"
)
# chapter split at the chapter level
toc2 <- tocChapters[[2]]
checkHeader(x = toc2, title = "2 Chapter", link = "2-chapter.html#chapter")
toc2Sect <- getSublist(toc2)
checkHeader(x = toc2Sect[[1]], title = "2.1 Section 1",
link = "2-chapter.html#section-1")
checkHeader(x = toc2Sect[[2]], title = "2.2 Section 2",
link = "2-chapter.html#section-2")
expect_length(object = getSublist(toc2Sect[[1]]), n = 0)
toc22Sub <- getSublist(toc2Sect[[2]])
checkHeader(x = toc22Sub[[1]], title = "2.2.1 Subsection 1",
link = "2-chapter.html#subsection-1")
checkHeader(x = toc22Sub[[2]], title = "2.2.2 Subsection 2",
link = "2-chapter.html#subsection-2")
# chapter split at the section level
toc3 <- tocChapters[[3]]
checkHeader(x = toc3, title = "3 Chapter",
link = "3-chapter.html#chapter")
toc3Sect <- getSublist(toc3)
checkHeader(x = toc3Sect[[1]], title = "3.1 Section 1",
link = "3.1-section-1.html#section-1")
checkHeader(x = toc3Sect[[2]], title = "3.2 Section 2",
link = "3.2-section-2.html#section-2")
expect_length(object = getSublist(toc3Sect[[1]]), n = 0)
toc32Sub <- getSublist(toc3Sect[[2]])
checkHeader(x = toc32Sub[[1]], title = "3.2.1 Subsection 1",
link = "3.2-section-2.html#subsection-1")
checkHeader(x = toc32Sub[[2]], title = "3.2.2 Subsection 2",
link = "3.2-section-2.html#subsection-2")
# appendix
tocAppendix <- tocChapters[[4]]
checkHeader(x = tocAppendix, title = "4 Appendix",
link = "4-appendix.html#appendix")
tocAppendixSections <- getSublist(tocAppendix)
checkHeader(x = tocAppendixSections, title = "4.1 Session information",
link = "4.1-session-information.html#session-information")
})
test_that("The chapter numbers are correctly set when there are more than 10 sections", {
secLevels <- c(1, rep(2, 11), rep(3, 2), rep(1, 10))
expect_equal(
object = clinDataReview:::getTocNumbering(levels = secLevels),
expected = c("1", paste0("1.", 1:11), paste0("1.11.", 1:2), as.character(2:11))
)
})
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context("Render a clinical data review report")
library(yaml)
library(parallel)
library(xml2)
test_that("Report titles are extracted for each config file", {
# get example config files
testPathConfig <- normalizePath(file.path("../files", "config"))
configFiles <- list.files(testPathConfig)
otherConfigs <- configFiles[!grepl("config.yml", configFiles)]
reportTitles <- clinDataReview:::checkReportTitles(configFiles, configDir = testPathConfig)
expect_type(reportTitles, "character")
expect_length(reportTitles, length(otherConfigs))
expect_named(reportTitles, otherConfigs)
})
test_that("An error is generated if the multiple reports have the same titles", {
# get example config files
testPathConfig <- normalizePath(file.path("../files", "config"))
configFiles <- list.files(testPathConfig)
configFilesError <- c(configFiles[1], configFiles[1])
expect_error(
clinDataReview:::checkReportTitles(configFilesError, configDir = testPathConfig),
"The title .+ is duplicated."
)
})
test_that("A warning is generated if a config is generated if a config file doesn't exist", {
# get example config files
testPathConfig <- normalizePath(file.path("../files", "config"))
configFiles <- list.files(testPathConfig)
configFilesWarning <- c(configFiles, "config-ciao")
expect_warning(
clinDataReview:::checkReportTitles(configFilesWarning, configDir = testPathConfig),
"Please check the spelling is correct"
)
})
test_that("Paths of markdown files are extracted correctly from the config files", {
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
configFiles <- list.files(testPathConfig)
testPathInterim <- file.path(testPathBase, "interim")
otherConfigs <- configFiles[!grepl("config.yml", configFiles)]
mdFiles <- clinDataReview:::getMdFromConfig(configFiles, intermediateDir = testPathInterim)
expect_type(mdFiles, "character")
expect_length(mdFiles, length(configFiles))
mdNames <- file.path(
testPathInterim,
c(
gsub("config-(.+).yml", "\\1.md", otherConfigs),
"index.md"
))
expect_identical(object = mdNames, expected = mdFiles)
})
test_that("Names of markdown files are extracted correctly from the config files when a custom index file is specified", {
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
configFiles <- list.files(testPathConfig)
otherConfigs <- configFiles[!grepl("config.yml", configFiles)]
testPathInterim <- file.path(testPathBase, "interim")
# Different name for indexPath
mdFilesIndex <- clinDataReview:::getMdFromConfig(
configFiles,
indexPath = "myIndex.Rmd",
intermediateDir = testPathInterim
)
expect_type(mdFilesIndex, "character")
expect_length(object = mdFilesIndex, n = length(configFiles))
mdNames <- file.path(
testPathInterim,
c(
gsub("config-(.+).yml", "\\1.md", otherConfigs),
"myIndex.md"
)
)
expect_identical(object = mdNames, expected = mdFilesIndex)
})
test_that("Names of markdown files are extracted correctly from the config files when a custom intermediate directory is specified", {
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
configFiles <- list.files(testPathConfig)
otherConfigs <- configFiles[!grepl("config.yml", configFiles)]
mdFilesInterim <- clinDataReview:::getMdFromConfig(configFiles, intermediateDir = "myDir")
expect_type(mdFilesInterim, "character")
expect_length(mdFilesInterim, length(configFiles))
mdNames <- file.path("myDir", c(
gsub("config-(.+).yml", "\\1.md", otherConfigs),
"index.md"
))
expect_identical(object = mdNames, expected = mdFilesInterim)
})
test_that("Parameters are extracted correctly from a general config file", {
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
listConfig <- getParamsFromConfig("config.yml", configDir = testPathConfig)
filePathGeneralConfig <- file.path(testPathConfig, "config.yml")
configFromYaml <- read_yaml(filePathGeneralConfig)
expect_type(listConfig, "list")
expect_length(configFromYaml, length(listConfig))
expect_identical(
object = listConfig,
expected = configFromYaml
)
})
test_that("Parameters are extracted correctly from a chapter-specific config file", {
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
listConfig <- getParamsFromConfig("config-adverseEvents-division.yml", configDir = testPathConfig)
configFromYamlGeneral <- read_yaml(file.path(testPathConfig, "config.yml"))
configFromYaml <- read_yaml(file.path(testPathConfig, "config-adverseEvents-division.yml"))
expect_type(listConfig, "list")
expect_length(
object = listConfig,
n = length(configFromYamlGeneral) + length(configFromYaml)
)
expect_mapequal(
object = listConfig,
expected = c(configFromYamlGeneral, configFromYaml)
)
})
test_that("An error is generated if the config directory is not available", {
configDir <- tempfile(pattern = "config")
expect_error(
getParamsFromConfig(configFile = "config.yml", configDir = configDir),
"Config directory: .+ doesn't exist."
)
})
test_that("An error is generated if a config file is not available", {
configDir <- tempfile(pattern = "config")
dir.create(configDir)
# get example general config file
testPathConfig <- normalizePath(file.path("../files", "config"))
file.copy(from = file.path(testPathConfig, "config.yml"), to = configDir)
expect_error(
getParamsFromConfig(configFile = "config-test.yml", configDir = configDir),
"File .+ cannot be found."
)
})
test_that("A warning is generated if the general config file is not available", {
configFileTemp <- tempfile(pattern = "config-", fileext = ".yml")
write_yaml(list(), configFileTemp)
expect_warning(
output <- getParamsFromConfig(
configFile = basename(configFileTemp),
configDir = dirname(configFileTemp)
),
"General config file: .+ not available"
)
expect_type(output, "list")
})
test_that("The creation of html file from the specified markdown files is successful", {
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
testPathInterim <- file.path(testPathBase, "interim")
# copy md file to temp directory
testDir <- tempfile("mdConversion")
dir.create(testDir)
tmp <- file.copy(from = testPathInterim, to = testDir, recursive = TRUE)
interimDir <- file.path(testDir, basename(testPathInterim))
# Md files
filePathMd <- file.path(interimDir, "adverseEvents-division.md")
expect_message(
htmlOutput <- clinDataReview:::convertMdToHtml(
mdFile = filePathMd,
indexPath = file.path(testPathBase, "index.Rmd"),
intermediateDir = interimDir,
outputDir = interimDir,
quiet = TRUE, # suppress printing of pandoc cmd line
),
"Convert the Markdown file.+to html.+"
)
expect_type(htmlOutput, "character")
expect_true(file.exists(htmlOutput))
expect_equal(normalizePath(dirname(htmlOutput)), normalizePath(interimDir))
})
test_that("The template name is successfully checked from correct config files", {
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
configFiles <- list.files(testPathConfig)
expect_silent(
checkedConfig <- clinDataReview:::checkTemplatesName(
configFiles = configFiles, configDir = testPathConfig
)
)
expect_type(checkedConfig, "character")
expect_identical(object = checkedConfig, expected = configFiles)
})
test_that("A warning is generated if a config file has no template name", {
testDir <- tempfile("config-templateName")
dir.create(testDir)
# create a general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(x = list(), file = configFileGeneral)
configFileTemplate <- tempfile(
pattern = "config-test", fileext = ".yml",
tmpdir = testDir
)
write_yaml(
x = list(reportTitle = "Title", reportTitleLevel = 2),
file = configFileTemplate
)
expect_warning(
clinDataReview:::checkTemplatesName(
configFiles = basename(configFileTemplate),
configDir = testDir
),
"Import of parameters from config file .+ failed with error:"
)
})
test_that("A warning is generated if config files with the same template name in different packages are used", {
testDir <- tempfile("config-sameTemplateName")
dir.create(testDir)
# create a general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(x = list(), file = configFileGeneral)
# create a first config file
configFileTemplate <- tempfile(pattern = "config-", fileext = ".yml", tmpdir = testDir)
write_yaml(
x = list(reportTitle = "Title", reportTitleLevel = 2,
template = "divisionTemplate", templatePackage = "custom"
),
file = configFileTemplate
)
configFileTemplate <- basename(configFileTemplate)
# create a second config file
configFileTemplateBis <- tempfile(pattern = "config-", fileext = ".yml", tmpdir = testDir)
write_yaml(
x = list(reportTitle = "Title", reportTitleLevel = 2,
template = "divisionTemplate", templatePackage = "clinDataReview"
),
file = configFileTemplateBis
)
configFileTemplateBis <- basename(configFileTemplateBis)
# check templates
configFileTemplates <- basename(c(configFileTemplate, configFileTemplateBis))
expect_warning(
output <- clinDataReview:::checkTemplatesName(
configFiles = configFileTemplates,
configDir = testDir
),
"The following config file.* are ignored, because the same template name is used"
)
expect_length(output, 0)
})
test_that("Session informations are merged successfully", {
sessionInfos <- list(sessionInfo(), sessionInfo())
sessionInfo <- do.call(clinDataReview:::merge.sessionInfo, sessionInfos)
expect_s3_class(sessionInfo, "sessionInfo")
})
test_that("Session informations with different elements are merged successfully", {
sessionInfos <- list(sessionInfo(), sessionInfo())
sessionInfos[[1]]$loadedOnly <- NULL
expect_silent(
sessionInfo <- do.call(clinDataReview:::merge.sessionInfo, sessionInfos)
)
expect_s3_class(sessionInfo, "sessionInfo")
})
test_that("The export of empty session infos to Markdown returns an empty output", {
expect_null(clinDataReview:::exportSessionInfoToMd(sessionInfos = NULL))
})
test_that("Session infos are successfully exported to Markdown", {
interimDir <- tempfile("interim")
sessionInfos <- list(sessionInfo(), sessionInfo())
mdFile <- clinDataReview:::exportSessionInfoToMd(
sessionInfos = sessionInfos,
intermediateDir = interimDir,
quiet = TRUE # suppress printing of pandoc cmd line
)
expect_type(mdFile, "character")
expect_true(file.exists(mdFile))
expect_identical(mdFile, file.path(interimDir, "sessionInfo.md"))
})
test_that("A clinical data report is created successfully via the specification of config files", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
configFiles <- list.files(testPathConfig)
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
outputDir <- file.path(testDir, "report")
# copy index file
file.copy(from = indexPath, to = testDir)
# copy configuration files
file.copy(from = testPathConfig, to = testDir, recursive = TRUE)
output <- render_clinDataReviewReport(
configFiles = configFiles,
configDir = testPathConfig,
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = outputDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
)
expect_type(output, "character")
expect_match(output, "introduction")
htmlFiles <- list.files(pattern = "html", outputDir)
expect_true(
any(grepl("1-introduction", htmlFiles))
)
})
test_that("A clinical data report is created successfully with a log file", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
# copy index file
file.copy(from = indexPath, to = testDir)
# copy configuration files
file.copy(from = testPathConfig, to = testDir, recursive = TRUE)
logPath <- file.path(testDir, "log.txt")
output <- render_clinDataReviewReport(
configDir = testPathConfig,
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = file.path(testDir, "report"),
logFile = logPath
)
expect_type(output, "character")
expect_match(output, "introduction")
expect_true(file.exists(logPath))
})
test_that("A clinical data report is created successfully via the specification of a config directory", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
testPathConfig <- file.path(testPathBase, "config")
configFiles <- list.files(testPathConfig)
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
outputDir <- file.path(testDir, "report")
# copy index file
file.copy(from = indexPath, to = testDir)
# copy configuration files
file.copy(from = testPathConfig, to = testDir, recursive = TRUE)
output <- render_clinDataReviewReport(
configFiles = NULL,
configDir = file.path(testDir, basename(testPathConfig)),
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = outputDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
)
expect_type(output, "character")
expect_match(output, "introduction")
htmlFiles <- list.files(pattern = "html", path = outputDir)
sectionName <- clinDataReview:::checkReportTitles(configFiles, configDir = testPathConfig)
sectionName <- gsub(" ", "-", sectionName)
expect_true(
any(grepl(sectionName, htmlFiles, ignore.case = TRUE))
)
})
test_that("A warning is generated if a specified config file doesn't exist", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
# copy index file
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
template = "divisionTemplate.Rmd",
templatePackage = "clinDataReview",
reportTitle = "Adverse events",
reportTitleLevel = 1
),
file = configFile1
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(
basename(configFile1),
"configFile2.yml"
)
),
file = configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1, "configFile2.yml")
configFiles <- basename(configFiles)
expect_warning(
output <- render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
inputDir = testDir,
intermediateDir = testDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
"configFile2.* cannot be found"
)
expect_type(output, "character")
expect_match(output, "introduction")
})
test_that("A warning is generated if a template report is already available", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
template = "divisionTemplate.Rmd",
templatePackage = "clinDataReview",
reportTitle = "Adverse events",
reportTitleLevel = 1
),
file = configFile1
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(
basename(configFile1)
)
),
file = configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1)
configFiles <- basename(configFiles)
# progress messages during execution
firstRun <- render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
inputDir = testDir,
intermediateDir = testDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
)
expect_warning(
secondRun <- render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
inputDir = testDir,
intermediateDir = testDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
"Document with similar name than specified template from"
)
expect_type(secondRun, "character")
expect_match(secondRun, regexp = "introduction")
})
test_that("A warning is generated if the creation of a chapter fails'", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
template = "templateWithError.Rmd",
sectionTitle = "Chapter with error"
),
file = configFile1
)
# create a Rmd file returning an error
cat(
"```{r}",
"stop('test')",
"```",
file = file.path(testDir, "templateWithError.Rmd"),
sep = "\n"
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(basename(configFile1))
),
file = configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1)
configFiles <- basename(configFiles)
expect_warning(
render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
intermediateDir = testDir,
inputDir = testDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
paste(
"Rendering of the .+ report for config file:.+configFile1.yml.+failed,",
"a report with only the section title is created.+")
)
})
test_that("A warning is generated if the template name is missing in a config file", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
reportTitle = "Adverse events",
reportTitleLevel = 1
),
file = configFile1
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(basename(configFile1))
),
file = configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1)
configFiles <- basename(configFiles)
expect_warning(
res <- render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
intermediateDir = testDir,
inputDir = testDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
"Template missing for config file: .+."
)
expect_type(res, "character")
expect_match(object = res, regexp = "introduction")
})
test_that("A warning is generated if the config parameters don't comply to the template specifications", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
template = "divisionTemplate.Rmd",
templatePackage = "clinDataReview"
),
file = configFile1
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(basename(configFile1))
),
file = configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1)
configFiles <- basename(configFiles)
expect_warning(
res <- render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
intermediateDir = testDir,
inputDir = testDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
"The report for the config file: .+ is not created because the check of the parameters failed"
)
expect_type(res, "character")
expect_match(object = res, regexp = "introduction")
})
test_that("A warning is generated if a template is not available in the specified package", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
template = "divisionTemplate.Rmd",
templatePackage = "myPackage"
),
file = configFile1
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(basename(configFile1))
),
file = configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1)
configFiles <- basename(configFiles)
expect_warning(
res <- render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
intermediateDir = testDir,
inputDir = testDir ,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
"Template file: .+ not available in.*myPackage.+ package."
)
expect_type(res, "character")
expect_match(object = res, regexp = "introduction")
})
test_that("A warning is generated if no config parameters are available", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
testDir <- tempfile("report")
dir.create(testDir)
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
template = "subjectProfile.Rnw",
templatePackage = "patientProfilesVis"
),
file = configFile1
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(basename(configFile1))
),
configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1)
configFiles <- basename(configFiles)
expect_warning(
res <- render_clinDataReviewReport(
configDir = testDir,
outputDir = testDir,
intermediateDir = testDir,
inputDir = testDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
"No config parameter available, input parameters for the report are not checked."
)
})
test_that("A warning is generated if some Markdown files are missing for conversion to html", {
testDir <- tempfile("report")
dir.create(testDir)
# get example config files
testPathBase <- normalizePath(path = "../files")
indexPath <- file.path(testPathBase, "index.Rmd")
file.copy(from = indexPath, to = testDir)
# file 1
configFile1 <- file.path(testDir, "configFile1.yml")
write_yaml(
x = list(
template = "divisionTemplate.Rmd",
templatePackage = "myPackage"
),
file = configFile1
)
# general config file
configFileGeneral <- file.path(testDir, "config.yml")
write_yaml(
x = list(
study = "Study name",
pathDataFolder = "path/to/data",
config = list(basename(configFile1))
),
file = configFileGeneral
)
configFiles <- c(configFileGeneral, configFile1)
configFiles <- basename(configFiles)
expect_error(
expect_warning(
postProcessReport(
configDir = testDir,
outputDir = testDir,
intermediateDir = testDir,
inputDir = testDir,
mdFiles = NULL,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
"Markdown file(s): .+ are missing, these files are ignored."
)
)
})
test_that("Config parameters with R code are correctly evaluated", {
configDir <- tempfile("config-r-eval")
dir.create(configDir)
# get example general config file
testPathConfig <- normalizePath(file.path("../files", "config"))
file.copy(from = file.path(testPathConfig, "config.yml"), to = configDir)
configFileTemp <- tempfile(pattern = "config-", fileext = ".yml", tmpdir = configDir)
write_yaml(list(param = structure("toString(c('a', 'b'))", tag = "!r")), configFileTemp)
# parameter is replaced by its evaluated version:
params <- getParamsFromConfig(
configFile = basename(configFileTemp),
configDir = configDir
)
expect_equal(params$param, "a, b")
})
test_that("Config parameters with R code and lazy-evaluation are imported non evaluated", {
configDir <- tempfile("config-r-eval-lazy")
dir.create(configDir)
# get example general config file
testPathConfig <- normalizePath(file.path("../files", "config"))
file.copy(from = file.path(testPathConfig, "config.yml"), to = configDir)
configFileTemp <- tempfile(pattern = "config-", fileext = ".yml", tmpdir = configDir)
write_yaml(list(param = structure("nrow(dataI)", tag = "!r-lazy")), configFileTemp)
params <- getParamsFromConfig(
configFile = basename(configFileTemp),
configDir = configDir
)
expect_type(params, "list")
expect_s3_class(params[["param"]], c("r-lazy", "character"))
expect_equal(as.character(params[["param"]]), "nrow(dataI)")
})
test_that("An error is generated if the R code specified in config parameters with lazy-evaluation contains errors", {
params <- list(nrowData = structure("nrow(customData)", class = "r-lazy"))
# error if R object is missing
expect_error(
forceParams(params),
".*customData.* not found"
)
})
test_that("Config parameters with R code and lazy-evaluation are correctly evaluated when requested", {
params <- list(nrowData = structure("nrow(customData)", class = "r-lazy"))
# parameter is replaced by its evaluated version:
customData <- data.frame(A = seq.int(2), B = c("A", "B"))
expect_silent(paramEvaluated <- forceParams(params))
expect_type(paramEvaluated, "list")
expect_named(paramEvaluated, "nrowData")
expect_equal(paramEvaluated$nrowData, nrow(customData))
})
test_that("A clinical data report is created successfully in parallel", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
testDir <- tempfile("report")
dir.create(testDir)
# create multiple config files
configDir <- file.path(testDir, "config")
dir.create(configDir)
nChapters <- 4
configFiles <- file.path(configDir,
paste0("config-division-", seq_len(nChapters), ".yml")
)
for(i in seq_len(nChapters)){
yaml::write_yaml(
list(
template = "divisionTemplate.Rmd",
templatePackage = "clinDataReview",
reportTitle = paste("Chapter", i),
reportTitleLevel = 1
),
configFiles[i]
)
}
# create general config file
yaml::write_yaml(
x = list(config = as.list(basename(configFiles))),
file = file.path(configDir, "config.yml")
)
# example index file
indexPath <- file.path(testDir, "index.Rmd")
cat(
"---",
"title: 'Clinical data report'",
"output: clinDataReview::gitbook_clinDataReview_report",
"---",
"# Introduction",
file = indexPath, sep = "\n"
)
outputDir <- file.path(testDir, "report")
output <- render_clinDataReviewReport(
configDir = configDir,
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = outputDir,
nCores = min(parallel::detectCores(), 2),
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
)
# check that all filenames are correct
htmlFiles <- list.files(pattern = ".html$", outputDir)
htmlFiles <- setdiff(htmlFiles, "404.html")
htmlFilesExp <- c(
"1-introduction.html",
paste0(2:5, "-chapter-", 1:4, ".html"),
"6-appendix.html"
)
expect_setequal(object = htmlFiles, expected = htmlFilesExp)
})
test_that("A clinical data report is created successfully in parallel with one chapter containing parallel execution", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
testDir <- tempfile("report")
dir.create(testDir)
configDir <- file.path(testDir, "config")
dir.create(configDir)
# create multiple config files
nChapters <- 4
configFiles <- file.path(configDir,
paste0("config-division-", seq_len(nChapters), ".yml")
)
for(i in seq_len(nChapters)){
yaml::write_yaml(
x = list(
template = "divisionTemplate.Rmd",
templatePackage = "clinDataReview",
reportTitle = paste("Chapter", i),
reportTitleLevel = 1
),
file = configFiles[i]
)
}
# create example chapter run in parallel
chapterParallel <- file.path(testDir, "chapter-parallel.Rmd")
cat(
"# Parallel",
"```{r eval = TRUE, echo = FALSE, class.output = \"testParallel\", comment = NA}",
"library(parallel)",
"cl <- makeCluster(2)",
"print(clusterApply(cl, 1:2, get('+'), 3))",
"stopCluster(cl = cl)",
"```",
file = chapterParallel, sep = "\n"
)
configFileParallel <- file.path(configDir, "config-parallel.yml")
yaml::write_yaml(
x = list(
template = basename(chapterParallel),
parallel = TRUE
),
file = configFileParallel
)
configFiles <- c(configFiles, configFileParallel)
# create general config file
yaml::write_yaml(
x = list(config = as.list(basename(configFiles))),
file = file.path(configDir, "config.yml")
)
# example index file
indexPath <- file.path(testDir, "index.Rmd")
cat(
"---",
"title: 'Clinical data report'",
"output: clinDataReview::gitbook_clinDataReview_report",
"---",
"# Introduction",
file = indexPath, sep = "\n"
)
# progress messages during execution
outputDir <- file.path(testDir, "report")
expect_error(
output <- render_clinDataReviewReport(
configDir = configDir,
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = outputDir,
nCores = min(parallel::detectCores(), 2),
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
),
NA
)
# check that all filenames are correct
htmlFiles <- list.files(pattern = "html", outputDir)
htmlFiles <- setdiff(htmlFiles, "404.html")
htmlFilesExp <- c(
"1-introduction.html",
paste0(2:5, "-chapter-", 1:4, ".html"),
"6-parallel.html",
"7-appendix.html"
)
expect_setequal(object = htmlFiles, expected = htmlFilesExp)
# check the content of the chapter run in parallel
htmlFileParallel <- xml2::read_xml(x = file.path(outputDir, "6-parallel.html"))
headXML <- xml2::xml_find_all(x = htmlFileParallel, xpath = ".//h1[span]")
expect_equal(object = xml2::xml_text(headXML), expected = "6 Parallel")
codeXML <- xml2::xml_find_all(
x = htmlFileParallel,
xpath = ".//pre[contains(@class, 'testParallel')]//code"
)
expect_match(object = xml2::xml_text(codeXML), regexp = "4.+5")
})
test_that("A report is correctly split at different chapter-specific levels", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
testDir <- tempfile("report")
dir.create(testDir)
# create multiple config files + template
template <- file.path(testDir, "chapter.Rmd")
cat(
"# Chapter",
"## Section 1",
"### Subsection 1",
"### Subsection 2",
"## Section 2",
file = template, sep = "\n"
)
configDir <- file.path(testDir, "config")
dir.create(configDir)
configFiles <- file.path(configDir,
paste0("config-division-", c("chapter", "section", "subsection"), ".yml")
)
for(i in seq_along(configFiles)){
yaml::write_yaml(
x = list(
template = basename(template),
split_by = as.integer(i),
reportTitle = paste("Chapter split at level", i)
),
file = configFiles[i]
)
}
# create general config file
yaml::write_yaml(
x = list(config = as.list(basename(configFiles))),
file = file.path(configDir, "config.yml")
)
# example index file
indexPath <- file.path(testDir, "index.Rmd")
cat(
"---",
"title: 'Clinical data report'",
"output:",
" clinDataReview::gitbook_clinDataReview_report:",
" split_by: 'section+number'",
"---",
"# Introduction",
file = indexPath, sep = "\n"
)
# progress messages during execution
outputDir <- file.path(testDir, "report")
output <- render_clinDataReviewReport(
configDir = configDir,
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = outputDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
)
expect_type(output, "character")
expect_match(output, "introduction")
# check that all filenames are correct
htmlFiles <- list.files(pattern = "html", outputDir)
htmlFiles <- setdiff(htmlFiles, "404.html")
htmlFilesExp <- c(
"1-introduction.html",
# split at chapter level
"2-chapter.html",
# split at the section level
"3-chapter.html",
"3.1-section-1.html", "3.2-section-2.html",
# split at the subsection level
"4-chapter.html",
"4.1-section-1.html", "4.1.1-subsection-1.html",
"4.1.2-subsection-2.html", "4.2-section-2.html",
"5-appendix.html",
"5.1-session-information.html"
)
expect_setequal(object = htmlFiles, expected = htmlFilesExp)
# check if content is correct
getHeaders <- function(file){
x <- xml2::read_xml(x = file)
headXML <- xml2::xml_find_all(x = x, xpath = ".//h1[span]|.//h2[span]|.//h3[span]")
headers <- xml2::xml_text(headXML)
return(headers)
}
# split at the chapter level
expect_setequal(
object = getHeaders(file = file.path(outputDir, "2-chapter.html")),
expected = c("2 Chapter", "2.1 Section 1", "2.1.1 Subsection 1",
"2.1.2 Subsection 2", "2.2 Section 2")
)
# split at the section level
expect_setequal(
object = getHeaders(file = file.path(outputDir, "3-chapter.html")),
expected = "3 Chapter"
)
expect_setequal(
object = getHeaders(file = file.path(outputDir, "3.1-section-1.html")),
expected = c("3.1 Section 1", "3.1.1 Subsection 1", "3.1.2 Subsection 2")
)
expect_setequal(
object = getHeaders(file = file.path(outputDir, "3.2-section-2.html")),
expected = "3.2 Section 2"
)
# split at the subsection level
expect_setequal(
object = getHeaders(file = file.path(outputDir, "4-chapter.html")),
expected = "4 Chapter"
)
expect_setequal(
object = getHeaders(file = file.path(outputDir, "4.1-section-1.html")),
expected = "4.1 Section 1"
)
expect_setequal(
object = getHeaders(file = file.path(outputDir, "4.1.1-subsection-1.html")),
expected = "4.1.1 Subsection 1"
)
expect_setequal(
object = getHeaders(file = file.path(outputDir, "4.1.2-subsection-2.html")),
expected = "4.1.2 Subsection 2"
)
expect_setequal(
object = getHeaders(file = file.path(outputDir, "4.2-section-2.html")),
expected = "4.2 Section 2"
)
})
test_that("The page titles are correctly set for a report", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
testDir <- tempfile("report")
dir.create(testDir)
# create multiple config files + template
template <- file.path(testDir, "chapter.Rmd")
cat(
"# Chapter",
"## Section 1",
"### Subsection 1",
"### Subsection 2",
"## Section 2",
file = template, sep = "\n"
)
configDir <- file.path(testDir, "config")
dir.create(configDir)
configFiles <- file.path(configDir,
paste0("config-division-", c("chapter", "section", "subsection"), ".yml")
)
for(i in seq_along(configFiles)){
yaml::write_yaml(
x = list(
template = basename(template),
split_by = as.integer(i),
reportTitle = paste("Chapter split at level", i)
),
file = configFiles[i]
)
}
# create general config file
yaml::write_yaml(
x = list(config = as.list(basename(configFiles))),
file = file.path(configDir, "config.yml")
)
# example index file
indexPath <- file.path(testDir, "index.Rmd")
cat(
"---",
"title: 'Clinical data report'",
"output:",
" clinDataReview::gitbook_clinDataReview_report:",
" split_by: 'section+number'",
"---",
"# Introduction",
file = indexPath, sep = "\n"
)
# progress messages during execution
outputDir <- file.path(testDir, "report")
output <- render_clinDataReviewReport(
configDir = configDir,
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = outputDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
)
getTitle <- function(file){
x <- xml2::read_xml(x = file)
titleXML <- xml2::xml_find_all(x = x, xpath = ".//title")
titles <- xml2::xml_text(titleXML)
return(titles)
}
# split at the chapter level
expect_equal(
object = getTitle(file = file.path(outputDir, "2-chapter.html")),
expected = "2 Chapter | Clinical data report"
)
# split at the section level
expect_equal(
object = getTitle(file = file.path(outputDir, "3-chapter.html")),
expected = "3 Chapter | Clinical data report"
)
expect_equal(
object = getTitle(file = file.path(outputDir, "3.1-section-1.html")),
expected = "3.1 Section 1 | Clinical data report"
)
expect_equal(
object = getTitle(file = file.path(outputDir, "3.2-section-2.html")),
expected = "3.2 Section 2 | Clinical data report"
)
# split at the subsection level
expect_setequal(
object = getTitle(file = file.path(outputDir, "4-chapter.html")),
expected = "4 Chapter | Clinical data report"
)
expect_equal(
object = getTitle(file = file.path(outputDir, "4.1-section-1.html")),
expected = "4.1 Section 1 | Clinical data report"
)
expect_equal(
object = getTitle(file = file.path(outputDir, "4.1.1-subsection-1.html")),
expected = "4.1.1 Subsection 1 | Clinical data report"
)
expect_equal(
object = getTitle(file = file.path(outputDir, "4.1.2-subsection-2.html")),
expected = "4.1.2 Subsection 2 | Clinical data report"
)
expect_equal(
object = getTitle(file = file.path(outputDir, "4.2-section-2.html")),
expected = "4.2 Section 2 | Clinical data report"
)
})
test_that("The table of contents is correctly set for a report", {
skip_on_cran()
# fix for: 'Using anchor_sections requires Pandoc 2.0+'
skip_if_not(
condition = rmarkdown::pandoc_available(version = "2.0"),
message = "pandoc 2.0 is not available"
)
testDir <- tempfile("report")
dir.create(testDir)
# create multiple config files + template
template <- file.path(testDir, "chapter.Rmd")
cat(
"# Chapter",
"## Section 1",
"## Section 2",
"### Subsection 1",
"### Subsection 2", # to test difference of level > 1 with next chapter
file = template, sep = "\n"
)
configDir <- file.path(testDir, "config")
dir.create(configDir)
configFiles <- file.path(configDir,
paste0("config-division-", c("chapter", "section"), ".yml")
)
for(i in seq_along(configFiles)){
yaml::write_yaml(
x = list(
template = basename(template),
split_by = as.integer(i),
reportTitle = paste("Chapter split at level", i)
),
file = configFiles[i]
)
}
# create general config file
yaml::write_yaml(
x = list(config = as.list(basename(configFiles))),
file = file.path(configDir, "config.yml")
)
# example index file
indexPath <- file.path(testDir, "index.Rmd")
cat(
"---",
"title: 'Clinical data report'",
"output:",
" clinDataReview::gitbook_clinDataReview_report:",
" split_by: 'section+number'",
"---",
"# Introduction",
file = indexPath, sep = "\n"
)
# progress messages during execution
outputDir <- file.path(testDir, "report")
output <- render_clinDataReviewReport(
configDir = configDir,
inputDir = testDir,
intermediateDir = file.path(testDir, "interim"),
outputDir = outputDir,
quiet = TRUE, # suppress printing of pandoc cmd line
verbose = FALSE
)
# import introduction and table of contents
book <- read_html(x = file.path(outputDir, "1-introduction.html"))
toc <- xml_find_all(book, ".//ul[@class='summary']")
checkHeader <- function(x, title, link){
head <- xml2::xml_find_first(x, ".//a")
expect_equal(object = xml2::xml_text(head), expected = title)
expect_equal(object = xml2::xml_attr(head, "href"), expected = link)
}
getSublist <- function(x){
xml_children(xml2::xml_find_first(x, ".//ul"))
}
tocChapters <- xml2::xml_children(toc)
# intro
checkHeader(
x = tocChapters[[1]],
title = "1 Introduction",
link = "1-introduction.html#introduction"
)
# chapter split at the chapter level
toc2 <- tocChapters[[2]]
checkHeader(x = toc2, title = "2 Chapter", link = "2-chapter.html#chapter")
toc2Sect <- getSublist(toc2)
checkHeader(x = toc2Sect[[1]], title = "2.1 Section 1",
link = "2-chapter.html#section-1")
checkHeader(x = toc2Sect[[2]], title = "2.2 Section 2",
link = "2-chapter.html#section-2")
expect_length(object = getSublist(toc2Sect[[1]]), n = 0)
toc22Sub <- getSublist(toc2Sect[[2]])
checkHeader(x = toc22Sub[[1]], title = "2.2.1 Subsection 1",
link = "2-chapter.html#subsection-1")
checkHeader(x = toc22Sub[[2]], title = "2.2.2 Subsection 2",
link = "2-chapter.html#subsection-2")
# chapter split at the section level
toc3 <- tocChapters[[3]]
checkHeader(x = toc3, title = "3 Chapter",
link = "3-chapter.html#chapter")
toc3Sect <- getSublist(toc3)
checkHeader(x = toc3Sect[[1]], title = "3.1 Section 1",
link = "3.1-section-1.html#section-1")
checkHeader(x = toc3Sect[[2]], title = "3.2 Section 2",
link = "3.2-section-2.html#section-2")
expect_length(object = getSublist(toc3Sect[[1]]), n = 0)
toc32Sub <- getSublist(toc3Sect[[2]])
checkHeader(x = toc32Sub[[1]], title = "3.2.1 Subsection 1",
link = "3.2-section-2.html#subsection-1")
checkHeader(x = toc32Sub[[2]], title = "3.2.2 Subsection 2",
link = "3.2-section-2.html#subsection-2")
# appendix
tocAppendix <- tocChapters[[4]]
checkHeader(x = tocAppendix, title = "4 Appendix",
link = "4-appendix.html#appendix")
tocAppendixSections <- getSublist(tocAppendix)
checkHeader(x = tocAppendixSections, title = "4.1 Session information",
link = "4.1-session-information.html#session-information")
})
test_that("The chapter numbers are correctly set when there are more than 10 sections", {
secLevels <- c(1, rep(2, 11), rep(3, 2), rep(1, 10))
expect_equal(
object = clinDataReview:::getTocNumbering(levels = secLevels),
expected = c("1", paste0("1.", 1:11), paste0("1.11.", 1:2), as.character(2:11))
)
})
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