inst/unitTests/test_validityFunctions.R

In AnnotationHubData: Transform public data resources into Bioconductor Data Structures

txdb <- GenomeInfoDb::loadTaxonomyDb()
txdb <- rbind(txdb, c(NA, NA, ""))

test_getSpeciesList <- function(){
    list <- getSpeciesList()
    checkTrue(length(list) == dim(txdb)[1])
}

test_validSpecies <- function(){

    checkTrue(validSpecies("Homo sapiens", verbose=FALSE))
    checkTrue(!validSpecies("Homo Sapiens", verbose=FALSE))
    checkTrue(validSpecies(NA_character_))
}

test_suggestSpecies <- function(){

    vl1 <- Reduce(`|`, lapply(txdb[2:3], grepl, pattern = "Dictyoglomus",
        ignore.case=TRUE))
    vl2 <- Reduce(`|`, lapply(txdb[2:3], grepl, pattern = "immobile",
        ignore.case=TRUE))

    out <- suggestSpecies(c("Dictyoglomus", "immobile"))
    checkTrue((length(which(vl1)) + length(which((vl2)))) == dim(out)[1])
}

test_validTaxId <- function(){

    checkTrue(is.null(AnnotationHubData::checkSpeciesTaxId(9606,
                                                           "Homo sapiens")))
    options(warn=2)
    checkException(AnnotationHubData::checkSpeciesTaxId(9999, "Homo sapiens"))
    options(warn=0)
}

test_validDispatchClass <- function(){

    checkTrue(validDispatchClass("GRanges"))
    checkTrue(validDispatchClass(c("GRanges", "Rda")))
    checkTrue(!validDispatchClass("somethingNotThere"))
    checkTrue(!validDispatchClass(c("GRanges", "somethingNotThere")))
}

test_FileLengths <- function(){

    checkTrue(AnnotationHubData:::.checkFileLengths(
        RDataPath = c("package/example1.bam", "package/example2.bai"),
        DispatchClass="BamFile"))
    checkException(AnnotationHubData:::.checkFileLengths(
        RDataPath = c("package/example1.bai", "package/example2.bam"),
        DispatchClass="BamFile"))
    checkException(AnnotationHubData:::.checkFileLengths(
        RDataPath = "package/example1.bam",
        DispatchClass="BamFile"))
     checkTrue(AnnotationHubData:::.checkFileLengths(
        RDataPath = "package/example1.rda",
        DispatchClass="Rda"))

}