From 9f957249c0bd21edf1ee3b3f1cd20dd6efc84c40 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Wed, 6 May 2020 08:41:14 +0200
Subject: [PATCH] R/api.R: Update file.exists assertions
* R/api.R <asserts>: file.exists -> isThingFile
---
R/api.R | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/R/api.R b/R/api.R
index a9e8a52..890258f 100644
--- a/R/api.R
+++ b/R/api.R
@@ -112,7 +112,7 @@ read_conf <- function(fn) {
yaml::yaml.load_file(fn)
}
## read_conf <- function(fn_conf) {
-## assert(file.exists(fn_conf),msg=paste("Unable to read the configuration file:", fn_conf))
+## assert(isThingFile(fn_conf),msg=paste("Unable to read the configuration file:", fn_conf))
## conf <- yaml::yaml.load_file(fn_conf)
## conf <- vrfy_conf(conf)
## conf
@@ -130,12 +130,12 @@ vrfy_conf <- function(conf) {
## ** Compound lists and sets
- assert(file.exists(fn_cmpd_sets),
+ assert(isThingFile(fn_cmpd_sets),
msg=paste("Cannot find the compound sets file:",fn_cmpd_sets))
- if (!is.null(fn_cmpd_known)) assert(file.exists(fn_cmpd_known),
+ if (!is.null(fn_cmpd_known)) assert(isThingFile(fn_cmpd_known),
msg=paste("Cannot find known compounds file:",fn_cmpd_known))
- if (!is.null(fn_cmpd_unk)) assert(file.exists(fn_cmpd_unk),
+ if (!is.null(fn_cmpd_unk)) assert(isThingFile(fn_cmpd_unk),
msg=paste("Cannot find unknown compounds file:",fn_cmpd_unk))
@@ -144,7 +144,7 @@ vrfy_conf <- function(conf) {
all_sets<-unique(df_sets$set)
fn_data <- conf$data
- assert(file.exists(fn_data),msg=paste("Data table does not exist:",fn_data))
+ assert(isThingFile(fn_data),msg=paste("Data table does not exist:",fn_data))
mzml <- file2tab(fn_data)
no_files <- which(mzml[,!file.exists(Files)])
--
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