diff --git a/R/state.R b/R/state.R
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+## Copyright (C) 2020,2021 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.
+
+
+##' @export
+new_state <- function() {
+ m <- new_conf()
+ init_state(m)
+}
+
+
+
+
+runtime_from_conf <- function(run,conf) {
+ lst_cmpl <- conf$compounds$lists
+ lst_fn_cmpl <- lapply(names(lst_cmpl),function (nm) {
+ bfn_cmpl <- lst_cmpl[[nm]]
+ fn <- file.path(run$paths$project,bfn_cmpl)
+ if (!file.exists(fn)) stop("File ", fn, " does not exist in ", run$paths$project," .")
+ fn
+ })
+ names(lst_fn_cmpl) <- names(lst_cmpl)
+ run$paths$compounds$lists <- lst_fn_cmpl
+
+ fn_sets <- file.path(run$paths$project,conf$compounds$sets[[1]]) #It's always only one.
+ if (!file.exists(fn_sets)) stop("File ", basename(fn_sets), " does not exist in ", run$paths$project," .")
+ run$paths$compounds$sets <- fn_sets
+
+ tmp <- conf$paths$datatab
+ datatab <- if (!is.null(tmp)) {
+ if (file.exists(tmp)) {
+ tmp
+ } else {
+ file.path(run$paths$project,tmp)
+ }
+ } else {
+ file.path(run$paths$project,FN_DATA_TAB)
+ }
+ if (!file.exists(datatab)) stop("A CSV file with data file entries does not exist (`paths$datatab' in config).")
+ datatab <- normalizePath(datatab)
+ run$paths$datatab <- datatab
+ run
+
+}
+
+
+## This helps decouple "cross-platform" configuration from the
+## (file-)system dependent facts.
+##' @export
+new_runtime_state <- function(project,conf=NULL) {
+
+ if (!is.character(project)) stop("Argument `project' must be a character string.")
+ if (!dir.exists(project)) stop('Project directory either does not exist, or is unreadable.')
+ project_path <- normalizePath(project)
+ project <- basename(project)
+ run <- list()
+ run$project <- project
+ run$paths$project <- project_path
+
+ run$paths$data <- if (is.null(conf$paths$data)) {
+ project_path
+ } else {
+ run$paths$data <- normalizePath(conf$paths$data)
+ }
+
+ if (!dir.exists(run$paths$data)) stop("Path to data directory either does not exist, or is inaccesible.")
+
+ if (!is.null(conf)) runtime_from_conf(run=run,conf=conf) else run
+
+}
+
+##' @export
+new_empty_project <- function(project) {
+ m <- new_state()
+ m$run <- new_runtime_state(project)
+ m
+}
+
+##' @export
+new_project <- function(project) {
+ m <- new_state()
+ m$run <- new_runtime_state(project)
+ fn_conf <- file.path(m$run$paths$project,FN_CONF)
+ m$conf <- read_conf(fn_conf)
+ m$run <- new_runtime_state(project,conf=m$conf)
+ m
+}
+
+
+##' @export
+new_rv_state <- function() react_v(m=list2rev(new_state()))
+
+
+write_conf <- function(m,fn) {
+ m$conf$paths$data <- get_fn_ftab(m)
+ if (NROW(m$input$tab$mzml)>0) tab2file(tab=m$input$tab$mzml,file=file.path(m$run$paths$project,FN_DATA_TAB))
+ yaml::write_yaml(x=m$conf,file=fn)
+
+
+
+}
+write_state <- function(m,fn_conf) {
+ write_conf(m,fn_conf)
+ tab2file(tab=m$input$tab$mzml,file=file.path(m$run$paths$project,FN_DATA_TAB))
+}
+
+read_conf <- function(fn) {
+ cf <- yaml::yaml.load_file(fn)
+ fnl <- cf$compounds$lists
+ if (length(fnl)>0) {
+ nms <- character(0)
+ for (i in 1:length(fnl)) {
+ nms <- gen_uniq_lab(nms,pref = 'L')
+ }
+ names(fnl) <- nms
+
+ }
+ cf$compounds$lists <- fnl
+ ## conf_trans(cf)
+ cf
+}
+
+
+
+##' @export
+get_fn_comp <- function(m) {
+ file.path(m$run$paths$project,FN_COMP_TAB)
+}
+
+##' @export
+get_fn_summ <- function(m) {
+ file.path(m$run$paths$project, FN_SUMM)
+}
+
+##' @export
+get_fn_extr <- function(m) {
+ file.path(m$run$paths$project, "extracted.rds")
+}
+
+##' @export
+get_fn_conf <- function(m) {
+ file.path(m$run$paths$project, FN_CONF)
+}
+
+
+##' @export
+get_fn_ftab <- function(m) {
+ file.path(m$run$paths$project, FN_DATA_TAB)
+}
+
+init_state <- function(m) {
+ m$out$tab <- list()
+ m$input$datafiles <- NULL
+ m$input$tab$mzml <- EMPTY_MZML
+ lab <- gen_uniq_lab(list(),pref="L")
+ m$input$tab$lists <- list()
+ m$input$tab[[lab[[1]]]] <- EMPTY_CMPD_LIST
+ m$out$tab$comp <- EMPTY_COMP_TAB
+ m
+}
+
+base_conf <- function () {
+ m <- list()
+ m$conf <- list(project=NA_character_,
+ compounds=list(lists=list(),
+ sets=""),
+ debug = F)
+ m
+}
+
+extr_conf <- function(m) {
+ m$conf$tolerance <- list("ms1 coarse"=MS1_ERR_COARSE,
+ "ms1 fine"=MS1_ERR_FINE,
+ "eic"=EIC_ERR,
+ "rt"=RT_EXTR_ERR)
+ m$conf$extract <- list(missing_precursor_info=DEF_CONF_MISSING_PCS)
+
+ m
+}
+
+presc_conf <- function(m) {
+ m$conf$prescreen <- list("ms1_int_thresh"=MS1_INT_THOLD,
+ "ms2_int_thresh"=MS2_INT_THOLD,
+ "s2n"=MS1_SN_FAC,
+ "ret_time_shift_tol"=RT_SHIFT_ERR)
+ m
+}
+
+fig_conf <- function(m) {
+ m$conf$figures$rt_min <- "NA_real_ min"
+ m$conf$figures$rt_max <- "NA_real_ min"
+ m$conf$figures$ext <- "pdf"
+ m
+}
+
+new_conf <- function() fig_conf(
+ presc_conf(
+ extr_conf(
+ base_conf())))