DESCRIPTION, envopts, errors: Add envopts.

* envopts.R: New file.

* DESCRIPTION: Update.

* errors: Replace variable error conditions with `check_' functions.

* man: Update.

DESCRIPTION

@@ -48,6 +48,7 @@ Collate:
     'resources.R'
     'errors.R'
     'mix.R'
+    'envopts.R'
     'state.R'
     'plotting.R'
     'extraction.R'

R/envopts.R

+## Copyright (C) 2020,2021,2023 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.
+
+
+## Description
+##
+## This file contains functions which manipulate per-system and
+## per-run parameters. For example, paths that may change from
+## computer to computer, such as the location of the MetFrag JAR file.
+
+
+
+
+#' @title Create a `envopts` Object
+#' @details A `envopts` object is Shinyscreen way to store settings
+#'     related to a specific computing environment. Information such
+#'     as the run time path to a MetFrag JAR will vary from one to
+#'     another setup and we need to convey this to the `shinyscreen`
+#'     pipeline.
+#' @param metfrag_db_dir `character(1)`, a path to the directory which contains MetFrag databases
+#' @param metfrag_jar  `character(1)`, a path to MetFrag JAR file
+#' @return An `envopts` object.
+#' @author Todor Kondić
+envopts <- function(metfrag_db_dir="",metfrag_jar="") {
+    res = list(metfrag=list())
+    class(res) = c("envopts","list") #Just to officially make it an
+                                     #object.
+
+    check_dir_absent(metfrag_db_dir,what="mf-db-dir")
+    res$metfrag$db_dir = metfrag_db_dir
+
+    check_file_absent(metfrag_jar,what="mf-jar")
+    res$metfrag$jar = metfrag_jar
+
+    res
+}

R/errors.R

@@ -12,12 +12,18 @@
 ## See the License for the specific language governing permissions and
 ## limitations under the License.
 
-errc_mf_jar_absent = errorCondition("MetFrag jar file specified, but cannot be found.", class = "mf-jar-absent")
-errc_mf_db_dir_absent = errorCondition("MetFrag DB directory specified, but cannot be found.", class = "mf-db-dir-absent")
-errc_mf_db_file_absent = errorCondition("MetFrag DB file specified, but cannot be found.", class = "mf-db-dir-absent")
+errc_conf_file_absent <- errorCondition("There is no config file in the project directory.",class="conf-file-absent")
 
-errc_projects_absent = errorCondition("User root directory (projects), currently does not exist.. Abort.", class= "projects-absent")
-errc_top_data_dir_absent = errorCondition("Data directory (top_data_dir) does not exist. Abort.",
-                                         class = "top-data-dir-absent")
+check_notastring <- function(value,what) {
+    if (!is.character(value)) stop(errorCondition(paste0("The value (",str(value),") of, ",what," is not a character vector."),class=paste0(what,'-notastring')))
+}
 
-errc_conf_file_absent <- errorCondition("There is no config file in the project directory.",class="conf-file-absent")
+check_dir_absent <- function(dir,what) {
+    check_notastring(dir,what)
+    if (nchar(dir)>0L && !dir.exists(dir)) stop(errorCondition(paste0("The ", what, " directory --- ", dir, "--- does not exist, or cannot be found."), class=paste0(what,'-absent')))
+}
+
+check_file_absent <- function(file,what) {
+    check_notastring(file,what)
+    if (nchar(file)>0L && !file.exists(file)) stop(errorCondition(paste0("The ", what, " file --- ", file, "--- does not exist, or cannot be found."), class=paste0(what,'-absent')))
+}

man/envopts.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/envopts.R
+\name{envopts}
+\alias{envopts}
+\title{Create a \code{envopts} Object}
+\usage{
+envopts(metfrag_db_dir = "", metfrag_jar = "")
+}
+\arguments{
+\item{metfrag_db_dir}{\code{character(1)}, a path to the directory which contains MetFrag databases}
+
+\item{metfrag_jar}{\code{character(1)}, a path to MetFrag JAR file}
+}
+\value{
+An \code{envopts} object.
+}
+\description{
+Create a \code{envopts} Object
+}
+\details{
+A \code{envopts} object is Shinyscreen way to store settings
+related to a specific computing environment. Information such
+as the run time path to a MetFrag JAR will vary from one to
+another setup and we need to convey this to the \code{shinyscreen}
+pipeline.
+}
+\author{
+Todor Kondić
+}