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fix: improve error handling and fix minor bugs #2

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fix: improve error handling and fix minor bugs #2

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2 changes: 1 addition & 1 deletion R/getEnrichrdb.R
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ getEnrichrdb <- function(org = c('human','fly','yeast','worm','zebrafish'),
res[[i]] = suppressWarnings(fst::read.fst(destfile))
}

res[['geneset_name']] <- NA
res[['geneset_name']] <- data.frame(term = character(0), name = character(0), stringsAsFactors = FALSE)

#--- add org for other use ---#
ensOrg_name <- ensOrg_name_data()
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2 changes: 1 addition & 1 deletion R/getHgDisease.R
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Expand Up @@ -59,7 +59,7 @@ getHgDisease <- function(source = c('do','disgenet','ncg_v7','ncg_v6','covid19')
data_dir, web_f_size, local_f_size)
res[[i]] = suppressMessages(fst::read.fst(destfile))
}else{
res[['geneset_name']] <- NA
res[['geneset_name']] <- data.frame(term = character(0), name = character(0), stringsAsFactors = FALSE)
}

#--- add org for other use ---#
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4 changes: 2 additions & 2 deletions R/getKEGG.R
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Expand Up @@ -26,7 +26,7 @@ getKEGG <- function(org = 'hsa',

# category <- tolower(category)
if(category %in% c('disease','drug','network') & org != 'hsa'){
stop(paste0('The categoty "',category, '" only support human...'))
stop(paste0('The category "',category, '" only supports human...'))
}

if(is.null(data_dir)){
Expand All @@ -41,7 +41,7 @@ getKEGG <- function(org = 'hsa',
for(i in c("geneset","geneset_name")){
# i = 'geneset'
url <- paste0(web.url(),sub_dir,category,'/',org,"_",i,".fst")
destfile <- paste0(data_dir, "/", org, "_",i,".fst")
destfile <- paste0(data_dir, "/", org, "_", category, "_", i, ".fst")
web_f_size <- check_web_size(url)
local_f_size <- file.size(destfile)
if(is.na(local_f_size)) local_f_size = 0
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2 changes: 1 addition & 1 deletion R/getMsigdb.R
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Expand Up @@ -172,7 +172,7 @@ getMsigdb <- function(org = 'human',
#------------------------------#
res <- list()
res[["geneset"]] <- geneset
res[["geneset_name"]] <- NA
res[["geneset_name"]] <- data.frame(term = character(0), name = character(0), stringsAsFactors = FALSE)

# Add organism for other use, preserving the original output behavior.
ensOrg_name <- ensOrg_name_data()
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7 changes: 4 additions & 3 deletions R/utilities.R
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Expand Up @@ -467,10 +467,11 @@ geneset_download <- function(url, destfile, data_dir,

if (!ok) {
if (!local_exists) {
message(
"No valid local cache is available.\n",
stop(
"Download failed and no local cache is available.\n",
"Please download manually via: ", url, "\n",
"Then save to: ", destfile
"Then save to: ", destfile,
call. = FALSE
)
}
return(invisible(FALSE))
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