library(igvR)
library(RUnit)
#----------------------------------------------------------------------------------------------------
runTests <- function()
{
test_url.exists()
test_supportedGenomes()
test_parseAndValidateGenomeSpec.stock()
test_parseAndValidateGenomeSpec.custom.http()
test_parseAndValidateGenomeSpec.custom.localFiles()
test_parseAndValidateGenomeSpec.custom.localFiles.sarsWithGFF3()
} # runTests
#----------------------------------------------------------------------------------------------------
test_url.exists <- function()
{
message(sprintf("--- test_url.exists"))
checkTrue(url.exists("https://google.com"))
checkTrue(!url.exists("https://google.com/bogusAndImprobableFilename.txt"))
checkTrue(url.exists("https://s3.amazonaws.com/igv.org.genomes/genomes.json"))
} # test_url.exists
#----------------------------------------------------------------------------------------------------
test_supportedGenomes <- function()
{
message(sprintf("--- test_supportedGenomes"))
cg <- currently.supported.stock.genomes()
checkTrue(length(cg) > 30)
cg.minimal <- currently.supported.stock.genomes(test=TRUE)
checkEquals(cg.minimal, c("hg38", "hg19", "mm10", "tair10", "rhos", "custom", "dm6", "sacCer3"))
} # test_supportedGenomes
#----------------------------------------------------------------------------------------------------
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()
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