From 9e0a4763be8a860645069d922048b26720171b06 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Mon, 27 Apr 2020 07:41:19 +0200
Subject: [PATCH] Add R/api.R
DESCRIPTION: New dependencies.
NAMESPACE: New imports.
R/api.R (read_conf,vrfy_conf): New functions.
---
DESCRIPTION | 3 +++
NAMESPACE | 1 +
R/api.R | 27 +++++++++++++++++++++++++++
3 files changed, 31 insertions(+)
create mode 100644 R/api.R
diff --git a/DESCRIPTION b/DESCRIPTION
index 9b8b892..00207dc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -49,6 +49,7 @@ Collate:
'mix.R'
'extraction.R'
'run.R'
+ 'api.R'
'shinyUI.R'
Depends:
RMassBank,
@@ -60,6 +61,8 @@ Imports:
yaml,
mzR,
MSnbase,
+ data.table,
+ assertthat,
ggplot2,
cowplot,
RColorBrewer,
diff --git a/NAMESPACE b/NAMESPACE
index 3dff728..ef97b55 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,3 +1,4 @@
# Generated by roxygen2: do not edit by hand
export(launch)
+export(read_conf)
diff --git a/R/api.R b/R/api.R
new file mode 100644
index 0000000..f05a1bb
--- /dev/null
+++ b/R/api.R
@@ -0,0 +1,27 @@
+## Copyright (C) 2020 by University of Luxembourg
+
+## Licensed under the Apache License, Version 2.0 (the "License");
+## you may not use this file except in compliance with the License.
+## You may obtain a copy of the License at
+
+## http://www.apache.org/licenses/LICENSE-2.0
+
+## Unless required by applicable law or agreed to in writing, software
+## distributed under the License is distributed on an "AS IS" BASIS,
+## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+## See the License for the specific language governing permissions and
+## limitations under the License.
+
+
+
+
+read_conf <- function(fn_conf) {
+ conf <- yaml::yaml.load_file(fn_conf)
+ conf <- vrfy_conf(conf)
+ conf
+}
+
+vrfy_conf <- function(conf) {
+ for (fn in unlist(conf,recursive=T)) assertthat::assert_that(file.exists(fn),msg=paste("Data file does not exist:",fn))
+ return(conf)
+}
--
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