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Merged
rcorces merged 2 commits into from
Jun 7, 2022
Merged

Dev better download #1453

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92bb44c
make tutorial downloads cleaner
rcorces Jun 7, 2022
cea4782
fix typo
rcorces Jun 7, 2022
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113 changes: 77 additions & 36 deletions R/InputData.R
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Original file line number Diff line number Diff line change
Expand Up @@ -11,57 +11,98 @@ getTutorialData <- function(
tutorial = "hematopoiesis",
threads = getArchRThreads()
){

#Validate
.validInput(input = tutorial, name = "tutorial", valid = "character")
.validInput(input = threads, name = "threads", valid = c("integer"))
#########

#Make Sure URL doesnt timeout
oldTimeout <- getOption('timeout')
options(timeout=100000)

if(tolower(tutorial) %in% c("heme","hematopoiesis")){

if(!dir.exists("HemeFragments")){

filesUrl <- c(
"https://jeffgranja.s3.amazonaws.com/ArchR/TestData/HemeFragments/scATAC_BMMC_R1.fragments.tsv.gz",
"https://jeffgranja.s3.amazonaws.com/ArchR/TestData/HemeFragments/scATAC_CD34_BMMC_R1.fragments.tsv.gz",
"https://jeffgranja.s3.amazonaws.com/ArchR/TestData/HemeFragments/scATAC_PBMC_R1.fragments.tsv.gz"
)

dir.create("HemeFragments", showWarnings = FALSE)

downloadFiles <- .safelapply(seq_along(filesUrl), function(x){
download.file(
url = filesUrl[x],
destfile = file.path("HemeFragments", basename(filesUrl[x]))
)
}, threads = min(threads, length(filesUrl)))

#check for success of file download
if(!all(unlist(downloadFiles) == 0)) {
stop("Error! Some tutorial files did not download successfully. Please try again.")
}
}
pathFragments <- "HemeFragments"

}else{

pathDownload <- "HemeFragments"

filesUrl <- c(
"https://jeffgranja.s3.amazonaws.com/ArchR/TestData/HemeFragments/scATAC_BMMC_R1.fragments.tsv.gz",
"https://jeffgranja.s3.amazonaws.com/ArchR/TestData/HemeFragments/scATAC_CD34_BMMC_R1.fragments.tsv.gz",
"https://jeffgranja.s3.amazonaws.com/ArchR/TestData/HemeFragments/scATAC_PBMC_R1.fragments.tsv.gz"
)

dir.create(pathDownload, showWarnings = FALSE)

downloadFiles <- .downloadFiles(filesUrl = filesUrl, pathDownload = pathDownload, threads = threads)

inputFiles <- list.files(pathDownload, pattern = "\\.gz$", full.names = TRUE)
names(inputFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathDownload, pattern = "\\.gz$"))
inputFiles <- inputFiles[!grepl(".tbi", inputFiles)]

}else if(tolower(tutorial) %in% c("multiome")){

filesUrl <- c(
"https://jeffgranja.s3.amazonaws.com/ArchR/TestData/Multiome/pbmc_sorted_3k.fragments.tsv.gz",
"https://jeffgranja.s3.amazonaws.com/ArchR/TestData/Multiome/pbmc_sorted_3k.filtered_feature_bc_matrix.h5",
"https://jeffgranja.s3.amazonaws.com/ArchR/TestData/Multiome/pbmc_unsorted_3k.fragments.tsv.gz",
"https://jeffgranja.s3.amazonaws.com/ArchR/TestData/Multiome/pbmc_unsorted_3k.filtered_feature_bc_matrix.h5"
)

pathDownload <- "Multiome"

dir.create(pathDownload, showWarnings = FALSE)

downloadFiles <- .downloadFiles(filesUrl = filesUrl, pathDownload = pathDownload, threads = threads)

fragFiles <- list.files(pathDownload, pattern = "\\.gz$", full.names = TRUE)
names(fragFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathDownload, pattern = "\\.gz$"))
fragFiles <- fragFiles[!grepl(".tbi", fragFiles)]
geneFiles <- list.files(pathDownload, pattern = "\\.h5$", full.names = TRUE)
names(geneFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathDownload, pattern = "\\.gz$"))

inputFiles <- c(fragFiles, geneFiles)

} else{

stop("There is no tutorial data for : ", tutorial)

}

#Set back URL Options
options(timeout=oldTimeout)

#Return Fragment Files
inputFiles <- list.files(pathFragments, pattern = ".gz", full.names = TRUE)
names(inputFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathFragments, pattern = ".gz"))
inputFiles <- inputFiles[!grepl(".tbi", inputFiles)]

inputFiles

}

#helper for file downloads
.downloadFiles <- function(filesUrl = NULL, pathDownload = NULL, threads = 1){
if(is.null(filesUrl)) {
stop("No value supplied to filesUrl in .downloadFiles()!")
}
if(is.null(pathDownload)) {
stop("No value supplied to pathDownload in .downloadFiles()!")
}
message(paste0("Downloading files to ",pathDownload,"..."))
downloadFiles <- .safelapply(seq_along(filesUrl), function(x){
if(!file.exists(file.path(pathDownload, basename(filesUrl[x])))){
message(paste0("Downloading file ", basename(filesUrl[x]),"..."))
download.file(
url = filesUrl[x],
destfile = file.path(pathDownload, basename(filesUrl[x]))
)
} else {
message(paste0("File exists! Skipping file ", basename(filesUrl[x]),"..."))
}
}, threads = min(threads, length(filesUrl)))

#check for success of file download
if(!all(unlist(downloadFiles) == 0)) {
stop("Some tutorial files did not download successfully. Please try again.")
}

downloadFiles

}

#' Get PBMC Small Test Fragments
Expand Down