Nothing
## RH 2019-09-28
#### SETUP ####
source("setup_ctrdata.R")
#### cache ####
expect_equal(
suppressMessages(
ctrdata:::ctrCache(
xname = "shouldNotExist",
verbose = TRUE
)), NULL)
expect_equal(
suppressMessages(
ctrdata:::ctrCache(
xname = "shouldNotExist",
xvalue = iris,
verbose = TRUE
)), iris)
expect_equal(
suppressMessages(
ctrdata:::ctrCache(
xname = "shouldNotExist",
verbose = TRUE
)), iris)
#### typeField ####
df <- data.frame(
"var2" = 2:5,
"var1" = c(1, "2", "NA", NA),
stringsAsFactors = FALSE)
expect_true(all(is.na(
ctrdata:::typeField(df[[2]], "anyname")[3:4])))
#### dfMergeVariablesRelevel ####
df1 <- data.frame(
"var1" = 1:3,
"var2" = 2:4,
stringsAsFactors = FALSE)
statusvalues <- list(
"Firstvalues" = c("12", "23"),
"Lastvalue" = c("34"))
df2 <- data.frame(var1 = c("A", "B", "C", NA),
var2 = c("D", "E", "", "G"))
# test
expect_error(
suppressWarnings(
dfMergeVariablesRelevel(list("var1", "var2"))),
"no appli")
# test
expect_message(
suppressWarnings(
dfMergeVariablesRelevel(
df = df1,
colnames = c("var1", "var2"))),
"More than one column had values, returning")
# test
expect_true(
"character" %in% class(
suppressWarnings(
suppressMessages(
dfMergeVariablesRelevel(
df = df1,
colnames = c("var1", "var2"))))))
# test
expect_equal(
suppressWarnings(
nchar(dfMergeVariablesRelevel(
df = df1,
colnames = c("var1", "var2")))),
c(5, 5, 5))
# test
expect_error(
suppressWarnings(
dfMergeVariablesRelevel(
df = cbind(df1, df1),
colnames = 1:3)))
# test
expect_error(
suppressWarnings(
dfMergeVariablesRelevel(
df = df1,
colnames = c("var1", "var2"),
levelslist = 1:2)),
"number of levels differs")
# test
expect_equal(
sum(grepl(" / ", suppressWarnings(suppressMessages(
dfMergeVariablesRelevel(
df = df2, colnames = c("var1", "var2")))))), 2L)
# test
expect_equal(
sum(grepl(" / ", suppressWarnings(suppressMessages(
dfMergeVariablesRelevel(
df = df2,
colnames = 'matches("var")'))))), 2L)
#### ctrGetQueryUrl ####
try(clipr::clear_clip(allow_non_interactive = TRUE), silent = TRUE)
# see also test_ctrdata_param_checks.R
expect_equal(
suppressWarnings(ctrGetQueryUrl(
"ThisDoesNotExist")),
NULL)
q <- "https://classic.clinicaltrials.gov/ct2/results?type=Intr&cond=cancer&age=0"
tmpTest <- suppressMessages(
ctrGetQueryUrl(
url = q))
# test
expect_true("data.frame" %in% class(tmpTest))
# test
expect_warning(
ctrGetQueryUrl(
url = "ThisDoesNotExist"),
"no clinical trial register search URL found")
# test if query= is added
expect_equal(
suppressMessages(
ctrGetQueryUrl(
url = "query=cancer&status=completed",
register = "EUCTR")),
suppressMessages(
ctrGetQueryUrl(
url = "cancer&status=completed",
register = "EUCTR"))
)
# test
expect_warning(
ctrGetQueryUrl(
url = "LETTERS"),
"no clinical trial register search URL found")
# test
expect_warning(
ctrGetQueryUrl(
url = "LETTERS",
register = "LETTERS"),
"no clinical trial register search URL found")
# test
expect_warning(
ctrGetQueryUrl(
url = "https://something",
register = "CTGOV"),
"no clinical trial register search URL")
# test
expect_error(
ctrGetQueryUrl(
url = c("https://onething", "https://something"),
register = "CTGOV"),
"is not a single character string")
# test
expect_error(
ctrGetQueryUrl(
url = "",
register = "EUCTR"),
"no clinical trial register search URL found")
# test
expect_message(
ctrGetQueryUrl(
url = "https://classic.clinicaltrials.gov/ct2/show/results/NCT00031447"),
"Found search query from CTGOV")
# test
expect_message(
ctrGetQueryUrl(
url = "https://classic.clinicaltrials.gov/ct2/show/NCT04372602?cond=COVID-19"),
"but also had search")
# test
expect_message(
ctrGetQueryUrl(
url = "https://classic.clinicaltrials.gov/ct2/show/results/NCT04372602?cond=COVID-19"),
"but also had search")
# test
expect_message(
ctrGetQueryUrl(
url = "https://classic.clinicaltrials.gov/ct2/show/record/NCT04372602?cond=COVID-19"),
"but also had search")
# test
expect_message(
ctrGetQueryUrl(
url = "https://clinicaltrials.gov/search?cond=neuroblastoma&intr=Investigational%20drug&aggFilters=ages:child,status:com&rank=8&sort=EnrollmentCount%3Adesc%2CNumArmGroups"),
"REST API")
# test
expect_message(
ctrGetQueryUrl(
url = "cond=neuroblastoma&intr=Investigational%20Drug&aggFilters=ages%3Achild%2Cstatus%3Acom&sort=EnrollmentCount%3Adesc%2CNumArmGroups",
register = "CTGOV"),
"REST API")
# test
expect_message(
ctrGetQueryUrl(
url =
"https://clinicaltrials.gov/study/NCT01467986?cond=neuroblastoma&intr=Investigational%20drug&aggFilters=ages:child,status:com&rank=2"),
"REST API")
# test
expect_message(
ctrGetQueryUrl(
url = "https://classic.clinicaltrials.gov/ct2/results?cond=neuroblastoma&rslt=With&recrs=e&age=0&intr=Drug"),
"Found search query from CTGOV")
# test
expect_message(
ctrGetQueryUrl(
url = "cond=Neuroblastoma&aggFilters=ages:child,results:with,studyType:int",
register = "CTGOV"),
"REST API")
# test
expect_equal(
ctrdata:::ctgovVersion(
url = data.frame(`no-query-term` = "something", check.names = FALSE),
register = "inout"),
"inout")
# test
expect_equal(
ctrdata:::ctgovVersion(
url = data.frame(`query-term` = "something", check.names = FALSE),
register = "inout"),
"inout")
#### ctrOpenSearchPagesInBrowser ####
if (!at_home()) exit_file("Reason: not at_home")
if (!checkInternet()) exit_file("Reason: no internet connectivity")
# test
expect_message(
ctrOpenSearchPagesInBrowser(url = q),
"Found search query")
q <- paste0("https://www.clinicaltrialsregister.eu/ctr-search/",
"search?query=&age=under-18&status=completed")
tmpTest <- suppressMessages(
ctrGetQueryUrl(
url = q))
# test
expect_true("data.frame" %in% class(tmpTest))
# test
expect_message(
ctrOpenSearchPagesInBrowser(q),
"Found search query")
# test
expect_message(
ctrOpenSearchPagesInBrowser(q),
"Found search query")
# test
expect_equal(
ctrOpenSearchPagesInBrowser(tmpTest),
paste0(q, "#tabs"))
# test
expect_true(
ctrOpenSearchPagesInBrowser(
copyright = TRUE))
# test
expect_equal(
ctrOpenSearchPagesInBrowser(
url = "https://www.clinicaltrials.gov/search?cond=neuroblastoma&intr=Investigational%20drug&aggFilters=ages:child,status:com&rank=200&sort=EnrollmentCount%3Adesc%2CNumArmGroups"
), "https://www.clinicaltrials.gov/search?cond=neuroblastoma&intr=Investigational drug&aggFilters=ages:child,status:com")
# test
expect_equal(
ctrOpenSearchPagesInBrowser(
url = "https://www.clinicaltrials.gov/study/NCT01467986?cond=neuroblastoma&intr=Investigational%20drug&aggFilters=ages:child,status:com&rank=2"
), "https://www.clinicaltrials.gov/study/NCT01467986#main-content")
# test
expect_equal(
ctrOpenSearchPagesInBrowser(
url = "https://euclinicaltrials.eu/app/#/view/2022-502267-37-00"
), "https://euclinicaltrials.eu/app/#/view/2022-502267-37-00")
# test
expect_equal(
ctrOpenSearchPagesInBrowser(
url = "https://www.clinicaltrialsregister.eu/ctr-search/trial/2015-005219-34/DE"
), "https://www.clinicaltrialsregister.eu/ctr-search/search?query=2015-005219-34#tabs")
# test
expect_equal(
ctrOpenSearchPagesInBrowser(
url = "https://www.isrctn.com/ISRCTN54460428?q=alzheimer&filters=&sort=&offset=29&totalResults=286&page=3&pageSize=10"
), "https://www.isrctn.com/ISRCTN54460428")
# test
expect_equal(
ctrOpenSearchPagesInBrowser(
url = "",
register = "CTGOV2"
), TRUE)
#### ctrLoadQueryIntoDb parameters ####
if (checkInternet()) {
# test
expect_warning(
ctrLoadQueryIntoDb(
queryterm = "somethingnonexisting",
register = "EUCTR",
euctrresultsfilespath = "something",
only.count = TRUE
), "deprecated"
)
# test
expect_warning(
ctrLoadQueryIntoDb(
queryterm = "somethingnonexisting",
register = "EUCTR",
euctrresultspdfpath = "something",
only.count = TRUE
), "deprecated"
)
# test
expect_warning(
ctrLoadQueryIntoDb(
queryterm = "somethingnonexisting",
register = "EUCTR",
parallelretrievals = 99L,
only.count = TRUE
), "ignored"
)
}
# test
expect_error(
ctrLoadQueryIntoDb(
queryterm = "somethingnonexisting",
querytoupdate = 1L,
), "cannot"
)
# test
expect_error(
ctrLoadQueryIntoDb(
queryterm = "somethingnonexisting",
register = 5L
), "does not seem"
)
# test
expect_error(
ctrLoadQueryIntoDb(
queryterm = "*",
register = "CTGOV"
), "unexpected character"
)
#### dfFindUniqueEuctrRecord ####
# test
expect_error(
ctrdata:::dfFindUniqueEuctrRecord(
df = list(1L)),
"Parameter df is not a data frame"
)
# test
expect_error(
ctrdata:::dfFindUniqueEuctrRecord(
df = iris),
"Data frame does not include"
)
# test
expect_error(
ctrdata:::dfFindUniqueEuctrRecord(
df = data.frame(
"_id" = "something",
"a2_eudract_number" = "something",
check.names = FALSE),
prefermemberstate = "something"),
"Value specified for prefermemberstate does not match"
)
#### dfName2Value ####
expect_error(
suppressMessages(
dfName2Value(
df = iris,
valuename = "something")),
"'df' does not seem to come from dfTrials2Long()")
expect_error(
suppressMessages(
dfName2Value(
df = iris,
valuename = "")),
"'valuename' must be specified")
#### dfTrials2Long ####
dF <- data.frame(
"_id" = paste0("NCT1234567", 1:5),
alpha1 = 1:5,
beta = 1:5,
gamma_1 = 1:5,
check.names = FALSE
)
dL <- suppressMessages(
dfTrials2Long(dF)
)
# test
expect_equal(nrow(dL), 15L)
expect_equal(unique(dL[["name"]]), names(dF)[-1])
dF <- suppressMessages(
dfName2Value(
df = dL,
valuename = "alp.*"))
# test
expect_equal(
nrow(dF), 5L)
expect_equal(
names(dF),
c("_id", "identifier", "name", "value"))
dF <- suppressMessages(
dfName2Value(
df = dL,
valuename = "[mp]",
wherename = "[a]",
wherevalue = "[3-4]"))
# test
expect_equal(
nrow(dF), 4L)
expect_equal(
names(dF),
c("_id", "identifier", "name", "value", "where"))
expect_true(
all(df[["name"]] %in% c("alpha1", "gamma_1")))
expect_true(
all(df[["value"]] %in% c(3, 4)))
# cleanup
rm(dF, dL)
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