base, resources, mix: Modify conf and state creation

* R/base.R(gen_uniq_lab): New function.

* R/mix.R(read_conf): Moved from api.R and updated. Now generates
  random names for the files in compound lists. This was needed
  because in its reactive form, a list of reactives needs names.

* R/resources.R(EMPTY_CONF): New parameter. Skeleton conf object.

R/base.R

@@ -44,3 +44,12 @@ print_table <- function (df) {
 }
 
 assert <- function(expr,msg) shiny::validate(shiny::need(expr,message=msg))
+
+
+gen_uniq_lab <- function(prev,pref='',suff='') {
+    l <- length(prev)
+    gen <- function() paste0(pref,as.integer(runif(1,min=l,max=2L*l+1L)),suff)
+    cand <- gen()
+    while (cand %in% prev) cand <- gen()
+    c(prev,cand)
+}

R/mix.R

@@ -699,12 +699,35 @@ write_state <- function(m,fn_conf) {
 }
 
 new_state <- function(conf,GUI) {
+read_conf <- function(fn) {
+    cf <- yaml::yaml.load_file(fn)
+    fnl <- cf$compound$lists
+    if (!is.null(fnl)) {
+        nms <- character(0)
+        for (i in 1:length(fnl)) {
+            nms <- gen_uniq_lab(nms,pref = 'L')
+        }
+        names(fnl) <- nms
+        
+    }
+    cf$compound$lists <- fnl
+
+    cf
+}
+
+new_conf <- function() EMPTY_CONF
+
+new_state <- function(conf=NULL,fn_conf="",GUI=F) {
+    assert(xor(!is.null(conf),nchar(fn_conf)!=0L),
+           msg="Provide either conf, or fn_conf, not both, not none.")
     m <- list()
-    m$conf <- conf
+    m$conf <- if (!is.null(conf)) conf else read_conf(fn_conf)
     m$GUI <- GUI
     m$out$tab <- list()
     m$input$tab$mzml <- EMPTY_MZML
-    m$input$tab$lists <- list(EMPTY_CMPD_LIST)
+    lab <- gen_uniq_lab(list(),pref="L")
+    m$input$tab$lists <- list()
+    m$input$tab[[lab[[1]]]] <- EMPTY_CMPD_LIST
     m
 }
 

R/resources.R

@@ -146,3 +146,12 @@ FN_DATA_TAB <- "data-files.csv"
 
 ## Default number of concurrent workers
 NO_WORKERS <- 2
+
+EMPTY_CONF <- list(project="",
+                   compounds=list(lists=list(),
+                                  sets=""),
+                   data="",
+                   tolerance=list("ms1 coarse"=MS1_ERR_COARSE,
+                                  "ms 1 fine"=MS1_ERR_FINE,
+                                  "eic"=EIC_ERR,
+                                  "rt"=RT_EXTR_ERR))