tests/testthat/test_class-LongTable.R

In CoreGx: Classes and Functions to Serve as the Basis for Other 'Gx' Packages

library(CoreGx)
library(testthat)
library(parallel)
library(data.table)

## FIXME:: Refactor into multiple test files?

# Configure required parameters
filePath <- 'merckLongTable.csv'
rowDataCols <- list(c(cell_line1='cell_line', BatchID='BatchID'))
colDataCols <- list(c(drug1='drugA_name', drug2='drugB_name',
    drug1dose='drugA Conc (uM)', drug2dose='drugB Conc (uM)'))
assayCols <- list(viability=paste0('viability', seq_len(4)),
                  viability_summary=c('mu/muMax', 'X/X0'))

context('Checking LongTable Class Methods.')

# ---- 1. buildLongTable
context('Testing buildLongTable function...')

context('Testing buildLongTable from a single table or file')
test_that('Can build LongTable from a file path', {
     longTable <- buildLongTable(from=filePath, rowDataCols,
        colDataCols, assayCols)
     expect_s4_class(longTable,'LongTable')
     expect_equal_to_reference(longTable, 'merckLongTable.rds')
})

merckDT <- fread('merckLongTable.csv', na.strings=c('NULL', 'NA', 'None', 'NULL'))
test_that('Can build longTable from a data.table', {
    longTable1 <- buildLongTable(from=merckDT, rowDataCols,
        colDataCols, assayCols)
    expect_s4_class(longTable1,'LongTable')
    expect_equal_to_reference(longTable1, 'merckLongTable.rds')
})

test_that('   from a data.frame', {
    longTable2 <- buildLongTable(from=setDF(merckDT),
        rowDataCols, colDataCols, assayCols)
    expect_s4_class(longTable2, 'LongTable')
    expect_equal_to_reference(longTable2, 'merckLongTable.rds')
})


context('Testing buildLongTable from mutliple tables or files')
# already know this works from previous test
longTable <- buildLongTable(from=filePath, rowDataCols, colDataCols, assayCols)

# update rowDataCols and colDataCols based on renamed columns in LongTable
rowDataColsOld <- rowDataCols
rowDataCols <- lapply(rowDataCols, names)
colDataColsOlds <- colDataCols
colDataCols <- lapply(colDataCols, names)

assayList <- assays(longTable, withDimnames=TRUE, metadata=TRUE)

## TODO:: Read in raw data for this step so we don't require working accessors

test_that('Can build LongTable from list of data.tables', {
    longTable1 <- buildLongTable(from=assayList, rowDataCols, colDataCols, assayCols)
    expect_s4_class(longTable1, 'LongTable')
    expect_equal_to_reference(longTable1, 'merckLongTable.rds')
})
test_that('Can build LongTable from list of data.frames', {
    for (assay in assayList) setDF(assay)
    longTable1 <- buildLongTable(from=assayList, rowDataCols, colDataCols, assayCols)
    expect_s4_class(longTable1, 'LongTable')
    expect_equal_to_reference(longTable1, 'merckLongTable.rds')
})


context('Testing buildLongTable errors correctly')

test_that('buildLongTable function errors if assayCols argument missing', {
    expect_error(buildLongTable(from=filePath, rowDataCols, colDataCols))
})

test_that('buildLongTable function errors if rowDataCols argument missing', {
    expect_error(buildLongTable(from=filePath, colDataCols=colDataCols,
        assayCols=assayCols))
})

test_that('builgLongTable function errors if colDataCols argument missing', {
    expect_error(buildLongTable(from=filePath, rowDataCols=rowDataCols,
        assayCols=assayCols))
})

test_that('    assayCols not in data', {
    expect_error(buildLongTable(from=filePath, rowDataCols, colDataCols, ))
})
## TODO:: Add more informative error cases


# ---- 2. Acessors methods
context('Testing LongTable accessor methods...')

# work correctly
context('LongTable accessors work correctly')
test_that('rowData works correctly', {
    # without keys
    rowData <- rowData(longTable)
    expect_equal(colnames(rowData), c('cell_line1', 'BatchID'))
    expect_s3_class(rowData, 'data.table')
    expect_equal_to_reference(rowData, 'merckLongTable.rowData.rds')
    # with keys
    rowDataKey <- rowData(longTable, key=TRUE)
    expect_equal(colnames(rowDataKey), c('cell_line1', 'BatchID', 'rowKey'))
    expect_equal_to_reference(rowDataKey, 'merckLongTable.rowDataWithKey.rds')
})
test_that('colData works correctly', {
    # without keys
    colData <- colData(longTable)
    expect_equal(colnames(colData), c("drug1", "drug2", "drug1dose", "drug2dose"))
    expect_s3_class(colData, 'data.table')
    expect_equal_to_reference(colData, 'merckLongTable.colData.rds')
    # with keys
    colDataKey <- colData(longTable, key=TRUE)
    expect_equal(colnames(colDataKey), c("drug1", "drug2", "drug1dose", "drug2dose", 'colKey'))
    expect_equal_to_reference(colDataKey, 'merckLongTable.colDataWithKey.rds')
})
test_that('assays works correctly', {
    assays <- assays(longTable)
    expect_equal(names(assays), assayNames(longTable))
    expect_equal_to_reference(assays, 'merckLongTable.assays.rds')
    assaysDimnames <- assays(longTable, withDimnames=TRUE)
    expect_equal_to_reference(assaysDimnames, 'merckLongTable.assaysDimnames.rds')
    assaysDimnamesMetadata <- assays(longTable, withDimnames=TRUE, metadata=TRUE)
    expect_equal_to_reference(assaysDimnamesMetadata, 'merckLongTable.assayDimnamesMetdata.rds')
})
test_that('assay works correctly', {
    assay <- assay(longTable, assayNames(longTable)[1])
    expect_equal_to_reference(assay, 'merckLongTable.assay.viability.rds')
    assayDimnames <- assay(longTable, assayNames(longTable)[1], withDimnames=TRUE)
    expect_equal_to_reference(assayDimnames, 'merckLongTable.assayDimnames.viability.rds')
    expect_equal(assay(longTable, 1), assay(longTable, 'viability'))
})


# error correctly
context('LongTable accessor methods error correctly')
test_that('assay function errors if assay is missing', {
    expect_error(assay(longTable, 'random'))
})
#test_that('assay function errors with logical', {
#
#})
#
## ----- 3. Setter Methods
#
## work correctly
#context('Testing LongTable setter methods...')
#context('LongTable setters work correctly')
#
## error correctly
#context('LongTable setter methods error correctly')


# ---- 4. Subset methods