Nothing
tests/testthat/test021_getStudiesSTSTDTC.R
In sendigR: Enable Cross-Study Analysis of 'CDISC' 'SEND' Datasets
################################################################################
## Test cases for the function getStudiesSTSTDTC.
##
## Expected data is located in: 021_expected_getStudiesSTSTDTC.xls
################################################################################
#### Prepare for test execution
rootPath <- '../data/'
getExpected <- function(sheetName) {
data.table::setkey(data.table::as.data.table(
readxl::read_xls(normalizePath(paste0(rootPath,
'021_expected_getStudiesSTSTDTC.xls')),
sheet=sheetName)), STUDYID)
}
db <- initEnvironment(dbType='sqlite',
dbPath=normalizePath(paste0(rootPath, 'test_db.db')))
#### Test cases 0x - execution without any input set of studies
test_that('01 - No input study list, no filtering',
{
# 1a - Report uncertainties
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
noFilterReportUncertain = TRUE),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG)])
# 1b - verify noFilterReportUncertain is TRUE as default
expect_equal(data.table::setkey(getStudiesSTSTDTC(db),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG)])
# 2 - Do not report uncertainties
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
noFilterReportUncertain = FALSE),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := NULL ])
# 3 - Parameter inclUncertain have no influence of reporting of uncertainties
# a - Do not report uncertainties
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
noFilterReportUncertain = FALSE,
inclUncertain = TRUE),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := NULL ])
# b - Report uncertainties
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
noFilterReportUncertain = TRUE,
inclUncertain = FALSE),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG)])
})
test_that('02 - No input study list, start day filter, open end',
{
# 1a - Full date, do not include uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2014-08-01',
inclUncertain = FALSE),
STUDYID),
getExpected('expect02_1')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL])
# 1b - Verify inclUncertain is FALSE as default
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2014-08-01'),
STUDYID),
getExpected('expect02_1')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL])
# 2 - Include uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2014-08-01',
inclUncertain = TRUE),
STUDYID),
getExpected('expect02_1'))
# 3 - Partial date, month
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2014-07',
inclUncertain = FALSE),
STUDYID),
getExpected('expect02_3'))
# 4 - Partial date, year
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2016',
inclUncertain = FALSE),
STUDYID),
getExpected('expect02_4'))
# 5 - Parameter noFilterReportUncertain have no influence of inclusion of unceratin rows
# a - Do not include uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2014-08-01',
inclUncertain = FALSE,
noFilterReportUncertain = TRUE),
STUDYID),
getExpected('expect02_1')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL])
# b - Include uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2014-08-01',
inclUncertain = TRUE,
noFilterReportUncertain = FALSE),
STUDYID),
getExpected('expect02_1'))
})
test_that('03 - No input study list, end day filter, open start',
{
# 1 - Full date
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
toDTC = '2015-12-31',
inclUncertain = FALSE),
STUDYID),
getExpected('expect03_1'))
# 2 - Partial date, month
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
toDTC = '2014-07',
inclUncertain = FALSE),
STUDYID),
getExpected('expect03_2'))
# 2 - Partial date, year
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
toDTC = '2014',
inclUncertain = FALSE),
STUDYID),
getExpected('expect03_1'))
})
test_that('04 - No input study list, start and end day filters',
{
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2010',
toDTC = '2014',
inclUncertain = FALSE),
STUDYID),
getExpected('expect04'))
})
#### Test cases 1x - execution with an input set of studies
# Prepare study lists for input
studyListIn <- data.table::data.table(STUDYID = c('CJ16050' , 'Study ID', 'GLP003' , 'Nimort-01', 'PDS2014' , 'PC201708'),
SDESIGN = c('PARALLEL', 'PARALLEL', 'PARALLEL', 'PARALLEL' , 'PARALLEL', 'PARALLEL'))
studyListInMsg <- data.table::data.table(STUDYID =
c('CJ16050' , 'Study ID', 'GLP003' , 'Nimort-01', 'PDS2014' , 'PC201708'),
SDESIGN =
c('PARALLEL' , 'PARALLEL', 'PARALLEL', 'PARALLEL' , 'PARALLEL', 'PARALLEL'),
NOT_VALID_MSG =
c('SDESIGN: A message', NA , NA , NA , NA , 'SDESIGN: Another message'))
studyListInUncertain <- data.table::data.table(STUDYID =
c('CJ16050' , 'Study ID', 'GLP003' , 'Nimort-01', 'PDS2014' , 'PC201708'),
SDESIGN =
c('PARALLEL' , 'PARALLEL', 'PARALLEL', 'PARALLEL' , 'PARALLEL', 'PARALLEL'),
UNCERTAIN_MSG =
c('SDESIGN: A message', NA , NA , NA , NA , 'SDESIGN: Another message'))
studyListInMsgUncertain <- data.table::data.table(STUDYID =
c('CJ16050' , 'Study ID', 'GLP003' , 'Nimort-01', 'PDS2014' , 'PC201708'),
SDESIGN =
c('PARALLEL' , 'PARALLEL', 'PARALLEL', 'PARALLEL' , 'PARALLEL' , 'PARALLEL'),
NOT_VALID_MSG =
c(NA , NA , NA , NA , 'TEST: Message', NA),
UNCERTAIN_MSG =
c('SDESIGN: A message', NA , NA , NA , NA , 'SDESIGN: Another message'))
# Execute test cases
test_that('11 - Input study list, no filters',
{
# 1 - Do not report uncertainties, input contains no not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListIn,
noFilterReportUncertain = FALSE),
STUDYID),
getExpected('expect11_1')[,NOT_VALID_MSG := NULL])
# 2 - Report uncertainties, input contains no not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListIn,
noFilterReportUncertain = TRUE),
STUDYID),
getExpected('expect11_1')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG) ])
# 3 - Report uncertainties, input contains a non-empty not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListInMsg,
noFilterReportUncertain = TRUE),
STUDYID),
getExpected('expect11_3')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG) ])
# TODO: Decide if NOT_VALID_MSG in input shall be kept (as currently) or dropped when
# function is called with noFilterReportUncertain = FALSE.
# Or maybe fail in check of input parameters
# 4 - Do not report uncertainties, input contains a non-empty not_valid_msg col an no uncertain rows
# expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
# studyList = studyListInMsg,
# noFilterReportUncertain = FALSE), STUDYID),
# getExpected('expect11_3')[,NOT_VALID_MSG := NULL ])
# TODO: Fix error: keep UNCERTAIN_MSAG and add NOT_VALID_MSG if relevant
#
# # 5 - Report uncertainties, input contains no not_valid_msg col and some uncertain rows
# expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
# studyList = studyListInUncertain,
# noFilterReportUncertain = TRUE),
# STUDYID),
# getExpected('expect11_5')[,UNCERTAIN_MSG := as.character(UNCERTAIN_MSG)])
#
# # 6 - Do not report uncertainties, input contains no not_valid_msg col and some uncertain rows
# expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
# studyList = studyListIn,
# noFilterReportUncertain = FALSE),
# STUDYID),
# getExpected('expect11_5'))
# TODO: Finalize expected data when decision in step 4 has been taken and implemented and bug in step 5 and 6 has been fixed.
#
# # 7 - Report uncertainties, input contains non-empty not_valid_msg col and some uncertain rows
# expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
# studyList = studyListInUncertain,
# noFilterReportUncertain = TRUE),
# STUDYID),
# getExpected('expect11_7')[,UNCERTAIN_MSG := as.character(UNCERTAIN_MSG)])
#
# # 8 - Do not report uncertainties, input contains non-empty not_valid_msg col and some uncertain rows
# expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
# studyList = studyListIn,
# noFilterReportUncertain = FALSE),
# STUDYID),
# getExpected('expect11_7'))
})
test_that('12 - Input study list, filters',
{
# 1 - Include uncertain rows, input contains no not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListIn,
fromDTC = '2014-08-01',
inclUncertain = TRUE),
STUDYID),
getExpected('expect12_1'))
# 2 - Do not include uncertain rows, input contains no not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListIn,
fromDTC = '2014-08-01'),
STUDYID),
getExpected('expect12_1')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - Include uncertain rows, input contains no not_valid_msg col and some uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListInUncertain,
fromDTC = '2014-08-01',
inclUncertain = TRUE),
STUDYID),
getExpected('expect12_3'))
# TODO: Decide how to act, when executed with inclUncertain = FALSE and input set contains uncertain rows
# - excluded these and drop col UNCERTAIN_MSG ?
# - keep uncertain rows from previuos steps....?
# # 4 - Do not include uncertain rows, input contains no not_valid_msg col and some uncertain rows
# expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
# studyList = studyListInUncertain,
# fromDTC = '2014-08-01',
# inclUncertain = FALSE),
# STUDYID),
# getExpected('expect12_3')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 5 - Include uncertain rows, input contains non-empty not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListInMsg,
fromDTC = '2014-08-01',
inclUncertain = TRUE),
STUDYID),
getExpected('expect12_5'))
# 6 - Do not include uncertain rows, input contains non-empty not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListInMsg,
fromDTC = '2014-08-01'),
STUDYID),
getExpected('expect12_5')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 7 - Include uncertain rows, input contains non-empty not_valid_msg col and some uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListInMsgUncertain,
fromDTC = '2010',
inclUncertain = TRUE),
STUDYID),
getExpected('expect12_7'))
# TODO: Same as step 4
# # 8 - Do not include uncertain rows, input contains non-empty not_valid_msg col and som uncertain rows
# expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
# studyList = studyListInMsgUncertain,
# fromDTC = '2010'),
# STUDYID),
# getExpected('expect12_7')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
})
#### Test sets 9x - error handling
test_that('91 - Validation of input parameters',
{
# Invalid filter dates
expect_error(getStudiesSTSTDTC(db, fromDTC = '214'),
regexp = 'not a valid .* date')
expect_error(getStudiesSTSTDTC(db , toDTC = '214'),
regexp = 'not a valid .* date')
expect_error(getStudiesSTSTDTC(db, fromDTC = '2014', toDTC = '20016'),
regexp = 'not a valid .* date')
})
disconnectDB(db)
Try the sendigR package in your browser
Any scripts or data that you put into this service are public.
sendigR documentation built on Aug. 18, 2022, 9:07 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
################################################################################
## Test cases for the function getStudiesSTSTDTC.
##
## Expected data is located in: 021_expected_getStudiesSTSTDTC.xls
################################################################################
#### Prepare for test execution
rootPath <- '../data/'
getExpected <- function(sheetName) {
data.table::setkey(data.table::as.data.table(
readxl::read_xls(normalizePath(paste0(rootPath,
'021_expected_getStudiesSTSTDTC.xls')),
sheet=sheetName)), STUDYID)
}
db <- initEnvironment(dbType='sqlite',
dbPath=normalizePath(paste0(rootPath, 'test_db.db')))
#### Test cases 0x - execution without any input set of studies
test_that('01 - No input study list, no filtering',
{
# 1a - Report uncertainties
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
noFilterReportUncertain = TRUE),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG)])
# 1b - verify noFilterReportUncertain is TRUE as default
expect_equal(data.table::setkey(getStudiesSTSTDTC(db),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG)])
# 2 - Do not report uncertainties
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
noFilterReportUncertain = FALSE),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := NULL ])
# 3 - Parameter inclUncertain have no influence of reporting of uncertainties
# a - Do not report uncertainties
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
noFilterReportUncertain = FALSE,
inclUncertain = TRUE),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := NULL ])
# b - Report uncertainties
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
noFilterReportUncertain = TRUE,
inclUncertain = FALSE),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG)])
})
test_that('02 - No input study list, start day filter, open end',
{
# 1a - Full date, do not include uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2014-08-01',
inclUncertain = FALSE),
STUDYID),
getExpected('expect02_1')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL])
# 1b - Verify inclUncertain is FALSE as default
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2014-08-01'),
STUDYID),
getExpected('expect02_1')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL])
# 2 - Include uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2014-08-01',
inclUncertain = TRUE),
STUDYID),
getExpected('expect02_1'))
# 3 - Partial date, month
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2014-07',
inclUncertain = FALSE),
STUDYID),
getExpected('expect02_3'))
# 4 - Partial date, year
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2016',
inclUncertain = FALSE),
STUDYID),
getExpected('expect02_4'))
# 5 - Parameter noFilterReportUncertain have no influence of inclusion of unceratin rows
# a - Do not include uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2014-08-01',
inclUncertain = FALSE,
noFilterReportUncertain = TRUE),
STUDYID),
getExpected('expect02_1')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL])
# b - Include uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2014-08-01',
inclUncertain = TRUE,
noFilterReportUncertain = FALSE),
STUDYID),
getExpected('expect02_1'))
})
test_that('03 - No input study list, end day filter, open start',
{
# 1 - Full date
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
toDTC = '2015-12-31',
inclUncertain = FALSE),
STUDYID),
getExpected('expect03_1'))
# 2 - Partial date, month
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
toDTC = '2014-07',
inclUncertain = FALSE),
STUDYID),
getExpected('expect03_2'))
# 2 - Partial date, year
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
toDTC = '2014',
inclUncertain = FALSE),
STUDYID),
getExpected('expect03_1'))
})
test_that('04 - No input study list, start and end day filters',
{
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
fromDTC = '2010',
toDTC = '2014',
inclUncertain = FALSE),
STUDYID),
getExpected('expect04'))
})
#### Test cases 1x - execution with an input set of studies
# Prepare study lists for input
studyListIn <- data.table::data.table(STUDYID = c('CJ16050' , 'Study ID', 'GLP003' , 'Nimort-01', 'PDS2014' , 'PC201708'),
SDESIGN = c('PARALLEL', 'PARALLEL', 'PARALLEL', 'PARALLEL' , 'PARALLEL', 'PARALLEL'))
studyListInMsg <- data.table::data.table(STUDYID =
c('CJ16050' , 'Study ID', 'GLP003' , 'Nimort-01', 'PDS2014' , 'PC201708'),
SDESIGN =
c('PARALLEL' , 'PARALLEL', 'PARALLEL', 'PARALLEL' , 'PARALLEL', 'PARALLEL'),
NOT_VALID_MSG =
c('SDESIGN: A message', NA , NA , NA , NA , 'SDESIGN: Another message'))
studyListInUncertain <- data.table::data.table(STUDYID =
c('CJ16050' , 'Study ID', 'GLP003' , 'Nimort-01', 'PDS2014' , 'PC201708'),
SDESIGN =
c('PARALLEL' , 'PARALLEL', 'PARALLEL', 'PARALLEL' , 'PARALLEL', 'PARALLEL'),
UNCERTAIN_MSG =
c('SDESIGN: A message', NA , NA , NA , NA , 'SDESIGN: Another message'))
studyListInMsgUncertain <- data.table::data.table(STUDYID =
c('CJ16050' , 'Study ID', 'GLP003' , 'Nimort-01', 'PDS2014' , 'PC201708'),
SDESIGN =
c('PARALLEL' , 'PARALLEL', 'PARALLEL', 'PARALLEL' , 'PARALLEL' , 'PARALLEL'),
NOT_VALID_MSG =
c(NA , NA , NA , NA , 'TEST: Message', NA),
UNCERTAIN_MSG =
c('SDESIGN: A message', NA , NA , NA , NA , 'SDESIGN: Another message'))
# Execute test cases
test_that('11 - Input study list, no filters',
{
# 1 - Do not report uncertainties, input contains no not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListIn,
noFilterReportUncertain = FALSE),
STUDYID),
getExpected('expect11_1')[,NOT_VALID_MSG := NULL])
# 2 - Report uncertainties, input contains no not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListIn,
noFilterReportUncertain = TRUE),
STUDYID),
getExpected('expect11_1')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG) ])
# 3 - Report uncertainties, input contains a non-empty not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListInMsg,
noFilterReportUncertain = TRUE),
STUDYID),
getExpected('expect11_3')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG) ])
# TODO: Decide if NOT_VALID_MSG in input shall be kept (as currently) or dropped when
# function is called with noFilterReportUncertain = FALSE.
# Or maybe fail in check of input parameters
# 4 - Do not report uncertainties, input contains a non-empty not_valid_msg col an no uncertain rows
# expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
# studyList = studyListInMsg,
# noFilterReportUncertain = FALSE), STUDYID),
# getExpected('expect11_3')[,NOT_VALID_MSG := NULL ])
# TODO: Fix error: keep UNCERTAIN_MSAG and add NOT_VALID_MSG if relevant
#
# # 5 - Report uncertainties, input contains no not_valid_msg col and some uncertain rows
# expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
# studyList = studyListInUncertain,
# noFilterReportUncertain = TRUE),
# STUDYID),
# getExpected('expect11_5')[,UNCERTAIN_MSG := as.character(UNCERTAIN_MSG)])
#
# # 6 - Do not report uncertainties, input contains no not_valid_msg col and some uncertain rows
# expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
# studyList = studyListIn,
# noFilterReportUncertain = FALSE),
# STUDYID),
# getExpected('expect11_5'))
# TODO: Finalize expected data when decision in step 4 has been taken and implemented and bug in step 5 and 6 has been fixed.
#
# # 7 - Report uncertainties, input contains non-empty not_valid_msg col and some uncertain rows
# expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
# studyList = studyListInUncertain,
# noFilterReportUncertain = TRUE),
# STUDYID),
# getExpected('expect11_7')[,UNCERTAIN_MSG := as.character(UNCERTAIN_MSG)])
#
# # 8 - Do not report uncertainties, input contains non-empty not_valid_msg col and some uncertain rows
# expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
# studyList = studyListIn,
# noFilterReportUncertain = FALSE),
# STUDYID),
# getExpected('expect11_7'))
})
test_that('12 - Input study list, filters',
{
# 1 - Include uncertain rows, input contains no not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListIn,
fromDTC = '2014-08-01',
inclUncertain = TRUE),
STUDYID),
getExpected('expect12_1'))
# 2 - Do not include uncertain rows, input contains no not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListIn,
fromDTC = '2014-08-01'),
STUDYID),
getExpected('expect12_1')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - Include uncertain rows, input contains no not_valid_msg col and some uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListInUncertain,
fromDTC = '2014-08-01',
inclUncertain = TRUE),
STUDYID),
getExpected('expect12_3'))
# TODO: Decide how to act, when executed with inclUncertain = FALSE and input set contains uncertain rows
# - excluded these and drop col UNCERTAIN_MSG ?
# - keep uncertain rows from previuos steps....?
# # 4 - Do not include uncertain rows, input contains no not_valid_msg col and some uncertain rows
# expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
# studyList = studyListInUncertain,
# fromDTC = '2014-08-01',
# inclUncertain = FALSE),
# STUDYID),
# getExpected('expect12_3')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 5 - Include uncertain rows, input contains non-empty not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListInMsg,
fromDTC = '2014-08-01',
inclUncertain = TRUE),
STUDYID),
getExpected('expect12_5'))
# 6 - Do not include uncertain rows, input contains non-empty not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListInMsg,
fromDTC = '2014-08-01'),
STUDYID),
getExpected('expect12_5')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 7 - Include uncertain rows, input contains non-empty not_valid_msg col and some uncertain rows
expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
studyList = studyListInMsgUncertain,
fromDTC = '2010',
inclUncertain = TRUE),
STUDYID),
getExpected('expect12_7'))
# TODO: Same as step 4
# # 8 - Do not include uncertain rows, input contains non-empty not_valid_msg col and som uncertain rows
# expect_equal(data.table::setkey(getStudiesSTSTDTC(db,
# studyList = studyListInMsgUncertain,
# fromDTC = '2010'),
# STUDYID),
# getExpected('expect12_7')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
})
#### Test sets 9x - error handling
test_that('91 - Validation of input parameters',
{
# Invalid filter dates
expect_error(getStudiesSTSTDTC(db, fromDTC = '214'),
regexp = 'not a valid .* date')
expect_error(getStudiesSTSTDTC(db , toDTC = '214'),
regexp = 'not a valid .* date')
expect_error(getStudiesSTSTDTC(db, fromDTC = '2014', toDTC = '20016'),
regexp = 'not a valid .* date')
})
disconnectDB(db)
Try the sendigR package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.