tests/testthat/test022_getStudiesSDESIGN.R

In sendigR: Enable Cross-Study Analysis of 'CDISC' 'SEND' Datasets

################################################################################
## Test cases for the function getStudiesSDESIGN.
##
## Expected data is 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)