inst/unitTests/test_genomeSpec.R

In paul-shannon/igvShiny: igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)

library(igvShiny)
library(RUnit)
library(shinytest2)
#----------------------------------------------------------------------------------------------------
runTests <- function()
{
    test_supportedGenomes()
    test_get_cas_genomes()
    test_parseAndValidateGenomeSpec.stock()
    test_parseAndValidateGenomeSpec.custom.http()
    test_parseAndValidateGenomeSpec.custom.localFiles()
    test_parseAndValidateGenomeSpec.custom.localFiles.sarsWithGFF3()

} # runTests
#----------------------------------------------------------------------------------------------------
test_supportedGenomes <- function()
{
    message(sprintf("--- test_supportedGenomes"))

    cg <- get_css_genomes()
    checkTrue(length(cg) > 30)

    cg.minimal <- get_css_genomes(test=TRUE)
    checkEquals(cg.minimal, c("hg38", "hg19", "mm10", "tair10", "rhos", "custom", "dm6", "sacCer3"))

} # test_supportedGenomes
#----------------------------------------------------------------------------------------------------
test_get_cas_genomes <- function()
{
    message(sprintf("--- test_get_cas_genomes"))

        #-------------------------------------------------------------------------
        # should return immediately, in contrast get_css_genomes
        # which requires an aws lookup
        #-------------------------------------------------------------------------

    t1 <- system.time(caasg <- get_cas_genomes())
    checkTrue(t1[["elapsed"]] < 0.1)
    checkTrue(all(c("hg38", "hg19", "mm10", "tair10", "custom", "dm6", "sacCer3") %in% caasg))

    t2 <- system.time(cssg  <- get_css_genomes())
    checkTrue(t2[["elapsed"]] > 0.01)

        #-------------------------------------------------------------------------
        # make sure that using one of the caasg also gets a nearly zero time
        # genomeSpec.  this ensures that the caasg is actually used.
        #-------------------------------------------------------------------------

    t3 <- system.time(parseAndValidateGenomeSpec(genomeName="hg38",  initialLocus="NDUFS2",
                                                 stockGenome=TRUE, dataMode="stock",
                                                 fasta=NA, fastaIndex=NA, genomeAnnotation=NA))
    t4 <- system.time(parseAndValidateGenomeSpec(genomeName="macFas5",  initialLocus="all",
                                                 stockGenome=TRUE, dataMode="stock",
                                                 fasta=NA, fastaIndex=NA, genomeAnnotation=NA))
    checkTrue(t3[["elapsed"]] < 0.1)
    checkTrue(t4[["elapsed"]] > 0.01)

} # test_get_cas_genomes
#----------------------------------------------------------------------------------------------------
test_parseAndValidateGenomeSpec.stock <- function()
{
    message(sprintf("--- test_parseAndValidateGenomeSpec.stock"))

    options <- parseAndValidateGenomeSpec(genomeName="hg38",  initialLocus="NDUFS2",
                                          stockGenome=TRUE, dataMode="stock",
                                          fasta=NA, fastaIndex=NA, genomeAnnotation=NA)

    checkEquals(sort(names(options)),
                c("annotation", "dataMode", "fasta", "fastaIndex", "genomeName",
                  "initialLocus", "stockGenome", "validated"))
    checkEquals(options[["genomeName"]], "hg38")
    checkTrue(options[["validated"]])
    checkTrue(options[["stockGenome"]])
    checkTrue(all(is.na(options[c("fasta", "fastaIndex", "annotation")])))

    error.caught <- tryCatch({
      suppressWarnings(
          options <- parseAndValidateGenomeSpec(genomeName="fubar99",  initialLocus="all")
          )
      FALSE;
      },
    error = function(e){
      TRUE;
      })
    checkTrue(error.caught)

} # test_parseAndValidateGenomeSpec.stock
#----------------------------------------------------------------------------------------------------
test_parseAndValidateGenomeSpec.custom.http <- function()
{
    message(sprintf("--- test_parseAndValidateGenomeSpec.custom.http"))

    base.url <- "https://gladki.pl/igvr/testFiles"
    fasta.file <- sprintf("%s/%s", base.url, "ribosomal-RNA-gene.fasta")
    fastaIndex.file <- sprintf("%s/%s", base.url, "ribosomal-RNA-gene.fasta.fai")
    annotation.file <- sprintf("%s/%s", base.url, "ribosomal-RNA-gene.gff3")


    options <- parseAndValidateGenomeSpec(genomeName="ribo",
                                          initialLocus="all",
                                          stockGenome=FALSE,
                                          dataMode="http",
                                          fasta=fasta.file,
                                          fastaIndex=fastaIndex.file,
                                          genomeAnnotation=annotation.file)

    checkEquals(sort(names(options)),
                c("annotation", "dataMode", "fasta", "fastaIndex", "genomeName",
                  "initialLocus", "stockGenome", "validated"))
    checkEquals(options[["genomeName"]], "ribo")
    checkTrue(options[["validated"]])
    checkTrue(!options[["stockGenome"]])
    checkTrue(all(!is.na(options[c("fasta", "fastaIndex", "annotation")])))

    checkEquals(options$fasta, fasta.file)
    checkEquals(options$fastaIndex, fastaIndex.file)
    checkEquals(options$annotation, annotation.file)
    checkEquals(options$dataMode, "http")

       #--------------------------------------------------------
       # now an intentional failure, with bogus fasta.file name
       #--------------------------------------------------------
    error.caught <- tryCatch({
       fasta.file <- sprintf("%s-bogus", fasta.file)
       options <- parseAndValidateGenomeSpec(genomeName="ribo-willFail",
                                             initialLocus="all",
                                             stockGenome=FALSE,
                                             dataMode="http",
                                             fasta=fasta.file,
                                             fastaIndex=fastaIndex.file,
                                             genomeAnnotation=annotation.file)
       FALSE;
       },
    error = function(e){
      TRUE;
      })

    checkTrue(error.caught)

} # test_parseAndValidateGenomeSpec.custom.http
#----------------------------------------------------------------------------------------------------
test_parseAndValidateGenomeSpec.custom.localFiles <- function()
{
    message(sprintf("--- test_parseAndValidateGenomeSpec.custom.localFiles"))

    data.directory <- system.file(package="igvShiny", "extdata")
    fasta.file <- file.path(data.directory, "ribosomal-RNA-gene.fasta")
    fastaIndex.file <- file.path(data.directory, "ribosomal-RNA-gene.fasta.fai")
    annotation.file <- file.path(data.directory, "ribosomal-RNA-gene.gff3")

    checkTrue(file.exists(fasta.file))
    checkTrue(file.exists(fastaIndex.file))
    checkTrue(file.exists(annotation.file))

    options <- parseAndValidateGenomeSpec(genomeName="ribosome local files",
                                          initialLocus="all",
                                          stockGenome=FALSE,
                                          dataMode="localFiles",
                                          fasta=fasta.file,
                                          fastaIndex=fastaIndex.file,
                                          genomeAnnotation=annotation.file)

    checkEquals(sort(names(options)),
                c("annotation", "dataMode", "fasta", "fastaIndex", "genomeName",
                  "initialLocus", "stockGenome", "validated"))
    checkEquals(options[["genomeName"]], "ribosome local files")
    checkTrue(options[["validated"]])
    checkTrue(!options[["stockGenome"]])
    checkTrue(all(!is.na(options[c("fasta", "fastaIndex", "annotation")])))

    checkEquals(options$fasta, fasta.file)
    checkEquals(options$fastaIndex, fastaIndex.file)
    checkEquals(options$annotation, annotation.file)
    checkEquals(options$dataMode, "localFiles")

       #--------------------------------------------------------
       # now an intentional failure, with bogus fasta.file name
       #--------------------------------------------------------
    error.caught <- tryCatch({
       fasta.file <- sprintf("%s-bogus", fasta.file)
       options <- parseAndValidateGenomeSpec(genomeName="ribo-willFail",
                                             initialLocus="all",
                                             stockGenome=FALSE,
                                             dataMode="http",
                                             fasta=fasta.file,
                                             fastaIndex=fastaIndex.file,
                                             genomeAnnotation=annotation.file)
       FALSE;
       },
    error = function(e){
      TRUE;
      })

    checkTrue(error.caught)

} # test_parseAndValidateGenomeSpec.custom.files
#----------------------------------------------------------------------------------------------------
test_parseAndValidateGenomeSpec.custom.localFiles.sarsWithGFF3 <- function()
{
    message(sprintf("--- test_parseAndValidateGenomeSpec.custom.localFiles.sarsWithGFF3"))

    data.directory <- system.file(package="igvShiny", "extdata", "sarsGenome")
    fasta.file <- file.path(data.directory, "Sars_cov_2.ASM985889v3.dna.toplevel.fa")
    fastaIndex.file <- file.path(data.directory, "Sars_cov_2.ASM985889v3.dna.toplevel.fa.fai")
    annotation.file <- file.path(data.directory, "Sars_cov_2.ASM985889v3.101.gff3")

    checkTrue(file.exists(fasta.file))
    checkTrue(file.exists(fastaIndex.file))
    checkTrue(file.exists(annotation.file))

    title <- "SARS-CoV-2"
    options <- parseAndValidateGenomeSpec(genomeName=title,
                                          initialLocus="all",
                                          stockGenome=FALSE,
                                          dataMode="localFiles",
                                          fasta=fasta.file,
                                          fastaIndex=fastaIndex.file,
                                          genomeAnnotation=annotation.file)

    checkEquals(sort(names(options)),
                c("annotation", "dataMode", "fasta", "fastaIndex", "genomeName",
                  "initialLocus", "stockGenome", "validated"))
    checkEquals(options[["genomeName"]], title)
    checkTrue(options[["validated"]])
    checkTrue(!options[["stockGenome"]])
    checkTrue(all(!is.na(options[c("fasta", "fastaIndex", "annotation")])))

    checkEquals(options$fasta, fasta.file)
    checkEquals(options$fastaIndex, fastaIndex.file)
    checkEquals(options$annotation, annotation.file)
    checkEquals(options$dataMode, "localFiles")


} # test_parseAndValidateGenomeSpec.custom.localFiles.sarsWithGFF3
#----------------------------------------------------------------------------------------------------

#    options <- parseAndValidateGenomeSpec(genomeName="hg38", initialLocus="all")
#      #                                    stockGenome=TRUE, dataMode=NA, fasta=NA, fastaIndex=NA, genomeAnnotation=NA)
#    checkEquals(names(options), "name")
#    checkEquals(options$name, "hg38")
#
#    error.caught <- tryCatch({
#        spec <- list(genomeName="fubar")
#        options <- parseAndValidateGenomeSpec(spec)
#        FALSE;
#        },
#    error = function(e){
#        TRUE;
#        })
#    checkTrue(error.caught)
#
#        #------------------------------------------------
#        # now an http explicit genomeSpec on our server
#        #------------------------------------------------
#
#    spec <- list(genomeName="customGenome",
#                 name="ribosome RNA",
#                 dataMode="http",
#                 fasta="https://gladki.pl/igvr/testFiles/ribosomal-RNA-gene.fasta",
#                 fastaIndex="https://gladki.pl/igvr/testFiles/ribosomal-RNA-gene.fasta.fai",
#                 annotation="https://gladki.pl/igvr/testFiles/ribosomal-RNA-gene.gff3")
#
#    options <- parseAndValidateGenomeSpec(spec)
#    checkEquals(options$name, "ribosome RNA")
#    checkEquals(options$fasta, "https://gladki.pl/igvr/testFiles/ribosomal-RNA-gene.fasta")
#    checkEquals(options$fastaIndex, "https://gladki.pl/igvr/testFiles/ribosomal-RNA-gene.fasta.fai")
#    checkEquals(options$annotation, "https://gladki.pl/igvr/testFiles/ribosomal-RNA-gene.gff3")
#
#        #----------------------------------------------------------------------------
#        # now an http explicit genomeSpec on our server, with a mis-spelled filename
#        #----------------------------------------------------------------------------
#
#    error.caught <- FALSE
#    spec$fasta <- sprintf("%s.bogus", spec$fasta)
#    error.caught <- tryCatch({
#        options <- parseAndValidateGenomeSpec(spec)
#        FALSE;
#        },
#        error = function(e){
#           TRUE;
#           })
#    checkTrue(error.caught)
#
#
#        #--------------------------------------------------------------------
#        # now n localFile explicit genomeSpec, files included in the package
#        #--------------------------------------------------------------------
#
#    data.dir <- system.file(package="igvShiny", "extdata")
#    fasta.file <- file.path(data.dir, "ribosomal-RNA-gene.fasta")
#    fasta.index.file <- file.path(data.dir, "ribosomal-RNA-gene.fasta.fai")
#    annotation.file <- file.path(data.dir, "ribosomal-RNA-gene.gff3")
#
#    spec <- list(genomeName="customGenome",
#                 name="ribosome RNA",
#                 dataMode="localFile",
#                 fasta=fasta.file,
#                 fastaIndex=fasta.index.file,
#                 annotation=annotation.file)
#
#    options <- parseAndValidateGenomeSpec(spec)
#    checkEquals(options$name, "ribosome RNA")
#    checkEquals(options$fasta, fasta.file)
#    checkEquals(options$fastaIndex, fasta.index.file)
#    checkEquals(options$annotation, annotation.file)
#
#        #------------------------------------------------------------------------------------------
#        # now n localFile explicit genomeSpec, files included in the package, mis-spelled filename
#        #------------------------------------------------------------------------------------------
#
#    error.caught <- FALSE
#    spec$annotation <- sprintf("%s.bogus", spec$annotation)
#    error.caught <- tryCatch({
#        options <- parseAndValidateGenomeSpec(spec)
#        FALSE;
#        },
#        error = function(e){
#           TRUE;
#           })
#    checkTrue(error.caught)
#----------------------------------------------------------------------------------------------------
if(!interactive())
    runTests()