Add R/api.R

DESCRIPTION: New dependencies.

NAMESPACE: New imports.

R/api.R (read_conf,vrfy_conf): New functions.

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,

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
 export(launch)
+export(read_conf)

R/api.R

+## 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)
+}