tests/testthat/test022_getStudiesSDESIGN.R
In phuse-org/sendigR: Enable Cross-Study Analysis of 'CDISC' 'SEND' Datasets
################################################################################
## Test cases for the function getStudiesSDESIGN with SQLite database
##
## Expected data are located in: 021_expected_getStudiesSDESIGN.xls
################################################################################
#### Prepare for test execution
rootPath <- '../data/'
getExpected <- function(sheetName) {
data.table::setkey(data.table::as.data.table(readxl::read_xls(normalizePath(
paste0(rootPath, '022_expected_getStudiesSDESIGN.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(getStudiesSDESIGN(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(getStudiesSDESIGN(db),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG)])
# 2 - Do not report uncertainties
expect_equal(data.table::setkey(getStudiesSDESIGN(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(getStudiesSDESIGN(db,
noFilterReportUncertain = FALSE,
inclUncertain = TRUE),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := NULL ])
# b - Report uncertainties
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
noFilterReportUncertain = TRUE,
inclUncertain = FALSE),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG)])
})
test_that('02 - No input study list, specified one filter value',
{
# 1a - Do not include uncertain rows, include all matching studies
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = 'PARALLEL',
exclusively = FALSE,
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(getStudiesSDESIGN(db,
exclusively = FALSE,
studyDesignFilter = 'PARALLEL'),
STUDYID),
getExpected('expect02_1')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL])
# 2 - Include uncertain rows, include all matching studies
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = 'PARALLEL',
exclusively = FALSE,
inclUncertain = TRUE),
STUDYID),
getExpected('expect02_1'))
# 3a - Do not include uncertain rows, include exclusive set of matching studies
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = 'PARALLEL',
exclusively = TRUE,
inclUncertain = FALSE),
STUDYID),
getExpected('expect02_3')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL])
# 3b - Verify exclusive is TRUE as default
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = 'PARALLEL',
inclUncertain = FALSE),
STUDYID),
getExpected('expect02_3')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL])
# 4 - Include uncertain rows, include exclusive set of matching studies
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = 'PARALLEL',
exclusively = TRUE,
inclUncertain = TRUE),
STUDYID),
getExpected('expect02_3'))
# 5 - Parameter noFilterReportUncertain have no influence of inclusion of uncertain rows
# a - Do not include uncertain rows
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = 'PARALLEL',
exclusively = FALSE,
inclUncertain = FALSE,
noFilterReportUncertain = TRUE),
STUDYID),
getExpected('expect02_1')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL])
# b - Include uncertain rows
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = 'PARALLEL',
exclusively = FALSE,
inclUncertain = TRUE,
noFilterReportUncertain = FALSE),
STUDYID),
getExpected('expect02_1'))
})
test_that('03 - No input study list, specified multiple filter values',
{
# 4 - include all matching studies
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = c('CROSSOVER', 'PARALLEL'),
exclusively = FALSE,
inclUncertain = FALSE),
STUDYID),
getExpected('expect03_1'))
# 4 - include all matching studies
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = c('CROSSOVER', 'PARALLEL'),
exclusively = TRUE,
inclUncertain = FALSE),
STUDYID),
getExpected('expect03_2'))
})
#
#
# #### Test cases 1x - execution with an input set of studies
#
# # Prepare study lists for input
studyListIn <- data.table::data.table(
STUDYID = c(
'CJ16050',
'CJUGSEND00',
'Study ID',
'GLP003',
'Nimort-01',
'PDS2014'),
STSTDTC = c(
'2021-01-01',
'2021-02-02',
'2021-03-03',
'2021-04-04',
'2021-05-05',
'2021-06-06'))
studyListInMsg <- data.table::data.table(
STUDYID = c(
'CJ16050',
'CJUGSEND00',
'Study ID',
'GLP003',
'Nimort-01',
'PDS2014'),
STSTDTC = c(
'2021-01-01',
'2021-02-02',
'2021-03-03',
'2021-04-04',
'2021-05-05',
'2021-06-06'),
NOT_VALID_MSG = c(
'STSTDTC: A message',
NA,
NA,
NA,
'STSTDTC: Another message',
NA))
studyListInUncertain <- data.table::data.table(
STUDYID = c(
'CJ16050',
'CJUGSEND00',
'Study ID',
'GLP003',
'Nimort-01',
'PDS2014'),
STSTDTC = c(
'2021-01-01',
'2021-02-02',
'2021-03-03',
'2021-04-04',
'2021-05-05',
'2021-06-06'),
UNCERTAIN_MSG = c(
'STSTDTC: A message',
NA,
NA,
NA,
'STSTDTC: Another message',
NA))
studyListInMsgUncertain <- data.table::data.table(
STUDYID = c(
'CJ16050',
'CJUGSEND00',
'Study ID',
'GLP003',
'Nimort-01',
'PDS2014'),
STSTDTC = c(
'2021-01-01',
'2021-02-02',
'2021-03-03',
'2021-04-04',
'2021-05-05',
'2021-06-06'),
NOT_VALID_MSG = c(
NA,
NA,
NA,
NA,
NA,
'TEST: Message'),
UNCERTAIN_MSG = c(
'STSTDTC: A message',
NA,
NA,
NA,
'STSTDTC: Another message',
NA))
# 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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(db,
# studyList = studyListIn,
# noFilterReportUncertain = FALSE),
# STUDYID),
# getExpected('expect11_7'))
})
test_that('12 - Input study list, filters',
{
# 1 - Include all matching studies, include uncertain rows, input contains no not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyList = studyListIn,
studyDesignFilter = 'PARALLEL',
exclusively = FALSE,
inclUncertain = TRUE),
STUDYID),
getExpected('expect12_1'))
# 2 - Include all matching studies, do not include uncertain rows, input contains no not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyList = studyListIn,
studyDesignFilter = 'PARALLEL',
exclusively = FALSE,
inclUncertain = FALSE),
STUDYID),
getExpected('expect12_1')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - Include exclusive set of matching studies
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyList = studyListIn,
studyDesignFilter = 'PARALLEL',
exclusively = TRUE,
inclUncertain = FALSE),
STUDYID),
getExpected('expect12_3'))
# 4 - Include uncertain rows, input contains no not_valid_msg col and some uncertain rows
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyList = studyListInUncertain,
studyDesignFilter = 'PARALLEL',
exclusively = FALSE,
inclUncertain = TRUE),
STUDYID),
getExpected('expect12_4'))
# 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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(db, fromDTC = '214'),
# regexp = 'not a valid .* date')
# expect_error(getStudiesSDESIGN(db , toDTC = '214'),
# regexp = 'not a valid .* date')
# expect_error(getStudiesSDESIGN(db, fromDTC = '2014', toDTC = '20016'),
# regexp = 'not a valid .* date')
# })
#
disconnectDB(db)
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################################################################################
## Test cases for the function getStudiesSDESIGN with SQLite database
##
## Expected data are located in: 021_expected_getStudiesSDESIGN.xls
################################################################################
#### Prepare for test execution
rootPath <- '../data/'
getExpected <- function(sheetName) {
data.table::setkey(data.table::as.data.table(readxl::read_xls(normalizePath(
paste0(rootPath, '022_expected_getStudiesSDESIGN.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(getStudiesSDESIGN(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(getStudiesSDESIGN(db),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG)])
# 2 - Do not report uncertainties
expect_equal(data.table::setkey(getStudiesSDESIGN(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(getStudiesSDESIGN(db,
noFilterReportUncertain = FALSE,
inclUncertain = TRUE),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := NULL ])
# b - Report uncertainties
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
noFilterReportUncertain = TRUE,
inclUncertain = FALSE),
STUDYID),
getExpected('expect01')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG)])
})
test_that('02 - No input study list, specified one filter value',
{
# 1a - Do not include uncertain rows, include all matching studies
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = 'PARALLEL',
exclusively = FALSE,
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(getStudiesSDESIGN(db,
exclusively = FALSE,
studyDesignFilter = 'PARALLEL'),
STUDYID),
getExpected('expect02_1')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL])
# 2 - Include uncertain rows, include all matching studies
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = 'PARALLEL',
exclusively = FALSE,
inclUncertain = TRUE),
STUDYID),
getExpected('expect02_1'))
# 3a - Do not include uncertain rows, include exclusive set of matching studies
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = 'PARALLEL',
exclusively = TRUE,
inclUncertain = FALSE),
STUDYID),
getExpected('expect02_3')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL])
# 3b - Verify exclusive is TRUE as default
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = 'PARALLEL',
inclUncertain = FALSE),
STUDYID),
getExpected('expect02_3')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL])
# 4 - Include uncertain rows, include exclusive set of matching studies
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = 'PARALLEL',
exclusively = TRUE,
inclUncertain = TRUE),
STUDYID),
getExpected('expect02_3'))
# 5 - Parameter noFilterReportUncertain have no influence of inclusion of uncertain rows
# a - Do not include uncertain rows
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = 'PARALLEL',
exclusively = FALSE,
inclUncertain = FALSE,
noFilterReportUncertain = TRUE),
STUDYID),
getExpected('expect02_1')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL])
# b - Include uncertain rows
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = 'PARALLEL',
exclusively = FALSE,
inclUncertain = TRUE,
noFilterReportUncertain = FALSE),
STUDYID),
getExpected('expect02_1'))
})
test_that('03 - No input study list, specified multiple filter values',
{
# 4 - include all matching studies
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = c('CROSSOVER', 'PARALLEL'),
exclusively = FALSE,
inclUncertain = FALSE),
STUDYID),
getExpected('expect03_1'))
# 4 - include all matching studies
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyDesignFilter = c('CROSSOVER', 'PARALLEL'),
exclusively = TRUE,
inclUncertain = FALSE),
STUDYID),
getExpected('expect03_2'))
})
#
#
# #### Test cases 1x - execution with an input set of studies
#
# # Prepare study lists for input
studyListIn <- data.table::data.table(
STUDYID = c(
'CJ16050',
'CJUGSEND00',
'Study ID',
'GLP003',
'Nimort-01',
'PDS2014'),
STSTDTC = c(
'2021-01-01',
'2021-02-02',
'2021-03-03',
'2021-04-04',
'2021-05-05',
'2021-06-06'))
studyListInMsg <- data.table::data.table(
STUDYID = c(
'CJ16050',
'CJUGSEND00',
'Study ID',
'GLP003',
'Nimort-01',
'PDS2014'),
STSTDTC = c(
'2021-01-01',
'2021-02-02',
'2021-03-03',
'2021-04-04',
'2021-05-05',
'2021-06-06'),
NOT_VALID_MSG = c(
'STSTDTC: A message',
NA,
NA,
NA,
'STSTDTC: Another message',
NA))
studyListInUncertain <- data.table::data.table(
STUDYID = c(
'CJ16050',
'CJUGSEND00',
'Study ID',
'GLP003',
'Nimort-01',
'PDS2014'),
STSTDTC = c(
'2021-01-01',
'2021-02-02',
'2021-03-03',
'2021-04-04',
'2021-05-05',
'2021-06-06'),
UNCERTAIN_MSG = c(
'STSTDTC: A message',
NA,
NA,
NA,
'STSTDTC: Another message',
NA))
studyListInMsgUncertain <- data.table::data.table(
STUDYID = c(
'CJ16050',
'CJUGSEND00',
'Study ID',
'GLP003',
'Nimort-01',
'PDS2014'),
STSTDTC = c(
'2021-01-01',
'2021-02-02',
'2021-03-03',
'2021-04-04',
'2021-05-05',
'2021-06-06'),
NOT_VALID_MSG = c(
NA,
NA,
NA,
NA,
NA,
'TEST: Message'),
UNCERTAIN_MSG = c(
'STSTDTC: A message',
NA,
NA,
NA,
'STSTDTC: Another message',
NA))
# 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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(db,
# studyList = studyListIn,
# noFilterReportUncertain = FALSE),
# STUDYID),
# getExpected('expect11_7'))
})
test_that('12 - Input study list, filters',
{
# 1 - Include all matching studies, include uncertain rows, input contains no not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyList = studyListIn,
studyDesignFilter = 'PARALLEL',
exclusively = FALSE,
inclUncertain = TRUE),
STUDYID),
getExpected('expect12_1'))
# 2 - Include all matching studies, do not include uncertain rows, input contains no not_valid_msg col and no uncertain rows
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyList = studyListIn,
studyDesignFilter = 'PARALLEL',
exclusively = FALSE,
inclUncertain = FALSE),
STUDYID),
getExpected('expect12_1')[is.na(UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - Include exclusive set of matching studies
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyList = studyListIn,
studyDesignFilter = 'PARALLEL',
exclusively = TRUE,
inclUncertain = FALSE),
STUDYID),
getExpected('expect12_3'))
# 4 - Include uncertain rows, input contains no not_valid_msg col and some uncertain rows
expect_equal(data.table::setkey(getStudiesSDESIGN(db,
studyList = studyListInUncertain,
studyDesignFilter = 'PARALLEL',
exclusively = FALSE,
inclUncertain = TRUE),
STUDYID),
getExpected('expect12_4'))
# 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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(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(getStudiesSDESIGN(db, fromDTC = '214'),
# regexp = 'not a valid .* date')
# expect_error(getStudiesSDESIGN(db , toDTC = '214'),
# regexp = 'not a valid .* date')
# expect_error(getStudiesSDESIGN(db, fromDTC = '2014', toDTC = '20016'),
# regexp = 'not a valid .* date')
# })
#
disconnectDB(db)
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