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tests/testthat/test034_getSubjSpeciesStrain.R
In sendigR: Enable Cross-Study Analysis of 'CDISC' 'SEND' Datasets
################################################################################
## Test cases for the function getSubjSpeciesStrain
##
## Expected output data is located in: 034_expected_getSubjSpeciesStrain.xls
## Input list of animals is also located in this Excel sheet
##
################################################################################
# Test data covers these situations:
#
# No SPECIES/STRAIN input filter criteria
# One SPECIES & no STRAIN input filter criteria
# Multiple SPECIES & no STRAIN input filter criteria
# One SPECIES/one STRAIN input filter criteria
# One SPECIES & mutliple STRAIN input filter criteria
# Mutiple SPECIES & one/mutliple STRAIN input filter criteria
# Valid SPECIES/STRAIN values (in TS, TX and DM)
# Invalid SPECIES/STRAIN CT value (in TS, TX and DM)
# Missing SPECIES/STRAIN value (in TS, TX and DM)
# Mismatch in SPECIES/STRAIN values between TS, TX and DM
# Without and with given filter criteria
# exclusively parameter values true and false respectively
# Inclusion/exclusion of uncertain values
#### Prepare for test execution
rootPath <- '../data/'
getExpected <- function(sheetName) {
data.table::setkeyv(data.table::as.data.table(
readxl::read_xls(normalizePath(paste0(rootPath,
'034_expected_getSubjSpeciesStrain.xls')),
sheet=sheetName))[,NO_AGE_MSG := as.character(NO_AGE_MSG)],
c('STUDYID','USUBJID'))
}
db <- initEnvironment(dbType='sqlite',
dbPath=normalizePath(paste0(rootPath, 'test_db.db')))
# Import set of animals used as input to getSubjSpeciesStrain
animalListIn1 <- getExpected('input_animalListIn')
animalListIn2 <- data.table::copy(animalListIn1)[,UNCERTAIN_MSG := NULL]
test_that('01 - No filtering',
{
animalListIn0 <- data.table::copy(animalListIn1)
data.table::setnames(animalListIn0, 'UNCERTAIN_MSG' ,'NOT_VALID_MSG')
# 1 - Report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn0,
noFilterReportUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect01')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG)])
# 2 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
noFilterReportUncertain = FALSE),
c('STUDYID','USUBJID')),
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::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
noFilterReportUncertain = FALSE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect01')[,NOT_VALID_MSG := NULL ])
# b - Report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn0,
noFilterReportUncertain = TRUE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect01')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG)])
# 4 - Parameter exclusively has no influence of returned list off animals
# a - FALSE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
exclusively = FALSE,
noFilterReportUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect01')[,NOT_VALID_MSG := NULL ])
# b - TRUE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
exclusively = TRUE,
noFilterReportUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect01')[,NOT_VALID_MSG := NULL ])
})
test_that('02 - Specified one species filter value',
{
# 1 - Report uncertainties, Exclusively is FALSE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = 'RAT',
exclusively = FALSE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect02'))
# 2 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = 'RAT',
exclusively = FALSE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect02')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - Parameter noFilterReportUncertain has no influence of reporting of uncertainties
# a - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = 'RAT',
exclusively = FALSE,
inclUncertain = FALSE,
noFilterReportUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect02')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# b - Report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = 'RAT',
exclusively = FALSE,
inclUncertain = TRUE,
noFilterReportUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect02'))
# 4 - exclusively is TRUE, report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = 'RAT',
exclusively = TRUE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect02_4'))
# 5 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = 'RAT',
exclusively = TRUE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect02_4')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
})
test_that('03 - Specified multiple species filter values',
{
# 1 - Report uncertainties, exclusively is FALSE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = c('RAT','monkey'),
exclusively = FALSE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect03'))
# 2 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = c('RAT','monkey'),
exclusively = FALSE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect03')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - exclusively is TRUE, report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = c('RAT','monkey'),
exclusively = TRUE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect03_3'))
# 4 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = c('RAT','monkey'),
exclusively = TRUE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect03_3')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
})
test_that('04 - Specified one species & one strain filter value',
{
# 1 - Report uncertainties, Exclusively is FALSE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = 'RAT',
strainFilter = 'wistar',
exclusively = FALSE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect04'))
# 2 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = 'RAT',
strainFilter = 'WISTAR',
exclusively = FALSE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect04')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - exclusively is TRUE, report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = 'RAT',
strainFilter = 'WISTAR',
exclusively = TRUE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect04_3'))
# 4 - Do report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = 'RAT',
strainFilter = 'WISTAR',
exclusively = TRUE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect04_3')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
})
test_that('05 - Specified one species & mutiple strain filter values',
{
# 1 - Report uncertainties, Exclusively is FALSE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = 'RAT',
strainFilter = c('WISTAR','SPRAGUE-DAWLEY'),
exclusively = FALSE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect05'))
# 2 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = 'RAT',
strainFilter = c('WISTAR','SPRAGUE-DAWLEY'),
exclusively = FALSE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect05')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - exclusively is TRUE, report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = 'RAT',
strainFilter = c('WISTAR','SPRAGUE-DAWLEY'),
exclusively = TRUE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect05_3'))
# 4 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = 'RAT',
strainFilter = c('WISTAR','SPRAGUE-DAWLEY'),
exclusively = TRUE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect05_3')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
})
test_that('06 - Specified multiple species & one strain filter values',
{
# 1 - Report uncertainties, Exclusively is FALSE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','DOG: BEAGLE', 'MONKEY: CYNOMOLGUS'),
exclusively = FALSE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect06'))
# 2 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','DOG: BEAGLE', 'MONKEY: CYNOMOLGUS'),
exclusively = FALSE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect06')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - exclusively is TRUE, report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','DOG: BEAGLE', 'MONKEY: CYNOMOLGUS'),
exclusively = TRUE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect06_3'))
# 4 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','DOG: BEAGLE', 'MONKEY: CYNOMOLGUS'),
exclusively = TRUE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect06_3')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
})
test_that('07 - Specified multiple species & mutiple strain filter values',
{
# 1 - Report uncertainties, Exclusively is FALSE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','RAT:SPRAGUE-DAWLEY','DOG:BEAGLE', 'MONKEY:CYNOMOLGUS'),
exclusively = FALSE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect07'))
# 2 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','RAT:SPRAGUE-DAWLEY','DOG:BEAGLE', 'MONKEY:CYNOMOLGUS'),
exclusively = FALSE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect07')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - exclusively is TRUE, report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','RAT:SPRAGUE-DAWLEY','DOG:BEAGLE', 'MONKEY:CYNOMOLGUS'),
exclusively = TRUE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect07_3'))
# 4 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','RAT:SPRAGUE-DAWLEY','DOG:BEAGLE', 'MONKEY:CYNOMOLGUS'),
exclusively = TRUE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect07_3')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
})
disconnectDB(db)
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################################################################################
## Test cases for the function getSubjSpeciesStrain
##
## Expected output data is located in: 034_expected_getSubjSpeciesStrain.xls
## Input list of animals is also located in this Excel sheet
##
################################################################################
# Test data covers these situations:
#
# No SPECIES/STRAIN input filter criteria
# One SPECIES & no STRAIN input filter criteria
# Multiple SPECIES & no STRAIN input filter criteria
# One SPECIES/one STRAIN input filter criteria
# One SPECIES & mutliple STRAIN input filter criteria
# Mutiple SPECIES & one/mutliple STRAIN input filter criteria
# Valid SPECIES/STRAIN values (in TS, TX and DM)
# Invalid SPECIES/STRAIN CT value (in TS, TX and DM)
# Missing SPECIES/STRAIN value (in TS, TX and DM)
# Mismatch in SPECIES/STRAIN values between TS, TX and DM
# Without and with given filter criteria
# exclusively parameter values true and false respectively
# Inclusion/exclusion of uncertain values
#### Prepare for test execution
rootPath <- '../data/'
getExpected <- function(sheetName) {
data.table::setkeyv(data.table::as.data.table(
readxl::read_xls(normalizePath(paste0(rootPath,
'034_expected_getSubjSpeciesStrain.xls')),
sheet=sheetName))[,NO_AGE_MSG := as.character(NO_AGE_MSG)],
c('STUDYID','USUBJID'))
}
db <- initEnvironment(dbType='sqlite',
dbPath=normalizePath(paste0(rootPath, 'test_db.db')))
# Import set of animals used as input to getSubjSpeciesStrain
animalListIn1 <- getExpected('input_animalListIn')
animalListIn2 <- data.table::copy(animalListIn1)[,UNCERTAIN_MSG := NULL]
test_that('01 - No filtering',
{
animalListIn0 <- data.table::copy(animalListIn1)
data.table::setnames(animalListIn0, 'UNCERTAIN_MSG' ,'NOT_VALID_MSG')
# 1 - Report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn0,
noFilterReportUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect01')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG)])
# 2 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
noFilterReportUncertain = FALSE),
c('STUDYID','USUBJID')),
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::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
noFilterReportUncertain = FALSE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect01')[,NOT_VALID_MSG := NULL ])
# b - Report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn0,
noFilterReportUncertain = TRUE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect01')[,NOT_VALID_MSG := as.character(NOT_VALID_MSG)])
# 4 - Parameter exclusively has no influence of returned list off animals
# a - FALSE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
exclusively = FALSE,
noFilterReportUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect01')[,NOT_VALID_MSG := NULL ])
# b - TRUE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
exclusively = TRUE,
noFilterReportUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect01')[,NOT_VALID_MSG := NULL ])
})
test_that('02 - Specified one species filter value',
{
# 1 - Report uncertainties, Exclusively is FALSE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = 'RAT',
exclusively = FALSE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect02'))
# 2 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = 'RAT',
exclusively = FALSE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect02')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - Parameter noFilterReportUncertain has no influence of reporting of uncertainties
# a - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = 'RAT',
exclusively = FALSE,
inclUncertain = FALSE,
noFilterReportUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect02')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# b - Report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = 'RAT',
exclusively = FALSE,
inclUncertain = TRUE,
noFilterReportUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect02'))
# 4 - exclusively is TRUE, report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = 'RAT',
exclusively = TRUE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect02_4'))
# 5 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = 'RAT',
exclusively = TRUE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect02_4')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
})
test_that('03 - Specified multiple species filter values',
{
# 1 - Report uncertainties, exclusively is FALSE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = c('RAT','monkey'),
exclusively = FALSE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect03'))
# 2 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = c('RAT','monkey'),
exclusively = FALSE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect03')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - exclusively is TRUE, report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = c('RAT','monkey'),
exclusively = TRUE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect03_3'))
# 4 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = c('RAT','monkey'),
exclusively = TRUE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect03_3')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
})
test_that('04 - Specified one species & one strain filter value',
{
# 1 - Report uncertainties, Exclusively is FALSE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = 'RAT',
strainFilter = 'wistar',
exclusively = FALSE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect04'))
# 2 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = 'RAT',
strainFilter = 'WISTAR',
exclusively = FALSE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect04')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - exclusively is TRUE, report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = 'RAT',
strainFilter = 'WISTAR',
exclusively = TRUE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect04_3'))
# 4 - Do report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = 'RAT',
strainFilter = 'WISTAR',
exclusively = TRUE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect04_3')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
})
test_that('05 - Specified one species & mutiple strain filter values',
{
# 1 - Report uncertainties, Exclusively is FALSE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = 'RAT',
strainFilter = c('WISTAR','SPRAGUE-DAWLEY'),
exclusively = FALSE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect05'))
# 2 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = 'RAT',
strainFilter = c('WISTAR','SPRAGUE-DAWLEY'),
exclusively = FALSE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect05')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - exclusively is TRUE, report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = 'RAT',
strainFilter = c('WISTAR','SPRAGUE-DAWLEY'),
exclusively = TRUE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect05_3'))
# 4 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = 'RAT',
strainFilter = c('WISTAR','SPRAGUE-DAWLEY'),
exclusively = TRUE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect05_3')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
})
test_that('06 - Specified multiple species & one strain filter values',
{
# 1 - Report uncertainties, Exclusively is FALSE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','DOG: BEAGLE', 'MONKEY: CYNOMOLGUS'),
exclusively = FALSE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect06'))
# 2 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','DOG: BEAGLE', 'MONKEY: CYNOMOLGUS'),
exclusively = FALSE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect06')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - exclusively is TRUE, report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','DOG: BEAGLE', 'MONKEY: CYNOMOLGUS'),
exclusively = TRUE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect06_3'))
# 4 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','DOG: BEAGLE', 'MONKEY: CYNOMOLGUS'),
exclusively = TRUE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect06_3')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
})
test_that('07 - Specified multiple species & mutiple strain filter values',
{
# 1 - Report uncertainties, Exclusively is FALSE
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','RAT:SPRAGUE-DAWLEY','DOG:BEAGLE', 'MONKEY:CYNOMOLGUS'),
exclusively = FALSE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect07'))
# 2 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','RAT:SPRAGUE-DAWLEY','DOG:BEAGLE', 'MONKEY:CYNOMOLGUS'),
exclusively = FALSE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect07')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
# 3 - exclusively is TRUE, report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn1,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','RAT:SPRAGUE-DAWLEY','DOG:BEAGLE', 'MONKEY:CYNOMOLGUS'),
exclusively = TRUE,
inclUncertain = TRUE),
c('STUDYID','USUBJID')),
getExpected('expect07_3'))
# 4 - Do not report uncertainties
expect_equal(data.table::setkeyv(getSubjSpeciesStrain(db,
animalList = animalListIn2,
speciesFilter = c('RAT','DOG','MONKEY'),
strainFilter = c('RAT:WISTAR','RAT:SPRAGUE-DAWLEY','DOG:BEAGLE', 'MONKEY:CYNOMOLGUS'),
exclusively = TRUE,
inclUncertain = FALSE),
c('STUDYID','USUBJID')),
getExpected('expect07_3')[!grepl('SpeciesStrain:',UNCERTAIN_MSG)][,UNCERTAIN_MSG := NULL ])
})
disconnectDB(db)
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