diff --git a/R/shiny-state.R b/R/shiny-state.R
index 78dd2ed9137f701b78f20ad9b46a371d73948565..43c190d578f68f92ea3ad3d0230b1b665885ca7b 100644
--- a/R/shiny-state.R
+++ b/R/shiny-state.R
@@ -263,28 +263,33 @@ unpack_app_state <- function(session,envopts,input,top_data_dir,project_path,pac
input2conf_setup <- function(input,gui,conf=list()) {
if (length(conf)==0L) {
conf$compounds <- list()
- conf$figures <- list()
- conf$prescreen <- list()
- conf$tolerance <- list()
- conf$extract <- list()
conf$summary_table <- list()
- conf$report <- list()
conf$debug <- F
}
conf$compounds$lists <- gui$compounds$lists
conf$compounds$sets <- gui$compounds$sets
+
+ conf$paths$data = gui$paths$data
+ conf
+}
+
+input2conf_extract <- function(input,conf) {
+ conf$tolerance = list()
+ conf$extract = list()
conf$tolerance[["ms1 fine"]] <- paste(input$ms1_fine,input$ms1_fine_unit)
conf$tolerance[["ms1 coarse"]] <- paste(input$ms1_coarse,input$ms1_coarse_unit)
conf$tolerance[["eic"]] <- paste(input$ms1_eic,input$ms1_eic_unit)
conf$tolerance[["rt"]] <- paste(input$ms1_rt_win,input$ms1_rt_win_unit)
conf$extract$missing_precursor_info <- input$missingprec
conf
+
}
input2conf_prescreen <- function(input,conf) {
+ conf$prescreen = list()
conf$prescreen[["ms1_int_thresh"]] <- input$ms1_int_thresh
conf$prescreen[["ms2_int_thresh"]] <- input$ms2_int_thresh
conf$prescreen[["s2n"]] <- input$s2n
@@ -293,6 +298,7 @@ input2conf_prescreen <- function(input,conf) {
}
input2conf_figures <- function(input,conf) {
+ conf$figures = list()
conf$figures$rt_min <- paste(input$plot_rt_min,input$plot_rt_min_unit)
conf$figures$rt_max <- paste(input$plot_rt_max,input$plot_rt_max_unit)
conf$figures$ext <- input$plot_ext
@@ -301,6 +307,7 @@ input2conf_figures <- function(input,conf) {
}
input2conf_report <- function(input,conf) {
+ conf$report = list()
conf$report$author <- input$rep_aut
conf$report$title <- input$rep_tit
conf
@@ -338,41 +345,59 @@ input2conf_metfrag <- function(input,conf) {
}
-input2conf <- function(input,gui,conf=list()) {
- conf = input2conf_setup(input,gui=gui,conf)
- conf = input2conf_prescreen(input,conf)
- conf = input2conf_figures(input,conf)
- conf = input2conf_report(input,conf)
- conf = input2conf_metfrag(input,conf)
- conf
+app_update_conf <- function(input,gui,envopts,fconf,m) {
+ for (fstrp in fconf) {
+ fstr = paste0("input2conf_",fstrp)
+ m$conf = do.call(fstr,list(input,conf=m$conf))
+ }
+ m$run <- new_runtime_state(project=gui$paths$project,
+ envopts = envopts,
+ conf=m$conf)
+ m
}
app_state2state <- function(input,gui,envopts,m=NULL) {
- if (is.null(m)) m <- new_project(project = gui$paths$project,
- envopts = envopts)
- ## m$run$paths <- shiny::reactiveValuesToList(gui$paths)
- m$conf = input2conf_setup(input,gui=gui)
- m$conf = input2conf_prescreen(input=input,conf=m$conf)
- m$conf = input2conf_figures(input,conf=m$conf)
- m$conf = input2conf_report(input,conf=m$conf)
- m$conf = input2conf_metfrag(input,conf=m$conf)
- m$conf$paths$data <- gui$paths$data
+ if (is.null(m)) m = new_project(project = gui$paths$project,
+ envopts = envopts)
+ m$conf = input2conf_setup(input=input,
+ gui=gui)
+
+
+ m = app_update_conf(input=input,
+ gui=gui,
+ envopts=envopts,
+ fconf = c("extract",
+ "prescreen",
+ "figures",
+ "report",
+ "metfrag"),
+ m=m)
+
+ ## m$conf = input2conf_setup(input,gui=gui)
+ ## m$conf = input2conf_prescreen(input=input,conf=m$conf)
+ ## m$conf = input2conf_figures(input,conf=m$conf)
+ ## m$conf = input2conf_report(input,conf=m$conf)
+ ## m$conf = input2conf_metfrag(input,conf=m$conf)
+
- m$run <- new_runtime_state(project=gui$paths$project,
- envopts = envopts,
- conf=m$conf)
+ ## m$run <- new_runtime_state(project=gui$paths$project,
+ ## envopts = envopts,
+ ## conf=m$conf)
m$input$tab$mzml <- gui2datatab(gui)
-
+
m
}
+
+
gen_comp_state <- function(input,gui) {
m <- app_state2state(input,gui)
run(m=m,phases=c("setup","mk_comp_tab"))
+
}
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index d547df90fdc4efcf5be7944202a46587e6f2765d..8ea32ec5cf4632cb02933ed8962e7317ea59da25 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -1131,6 +1131,8 @@ mk_shinyscreen_server <- function(projects,init) {
observeEvent(input$extract_b,{
rvs$m = app_state2state(input,rvs$gui,envopts = init$envopts, m=rvs$m) # Update params from GUI.
+ ## Clear out prescreen data if any.
+ rvs$m$out$tab$summ=EMPTY_SUMM
m = rvs$m
shinymsg("Extraction has started. This may take a while.")
rvs$status$ms1_coarse_stat = m$conf$tolerance[["ms1 coarse"]]
@@ -1138,9 +1140,8 @@ mk_shinyscreen_server <- function(projects,init) {
rvs$status$ms1_eic_stat = m$conf$tolerance[["eic"]]
rvs$status$rt_stat = m$conf$tolerance[["rt"]]
rvs$status$is_extracted_stat = "In progress."
+ rvs$status$is_qa_stat = "No."
rv_extr_flag(T)
- rv_presc_flag(F)
-
})
observe({
@@ -1168,7 +1169,14 @@ mk_shinyscreen_server <- function(projects,init) {
observeEvent(input$presc_b,{
if (NROW(rvs$m$extr$ms1)>0L) {
- rvs$m = app_state2state(input,rvs$gui,envopts = init$envopts, m=rvs$m) # Update params from GUI.
+ ## Update just prescreening conf.
+ rvs$m = app_update_conf(input=input,
+ gui=rvs$gui,
+ envopts=init$envopts,
+ fconf="prescreen",
+ m=rvs$m)
+
+ ## rvs$m = app_state2state(input,rvs$gui,envopts = init$envopts, m=rvs$m) # Update params from GUI.
rvs$status$ms1_int_thresh_stat = rvs$m$conf$prescreen[["ms1_int_thresh"]]
rvs$status$ms2_int_thresh_stat = rvs$m$conf$prescreen[["ms2_int_thresh"]]
rvs$status$s2n_stat = rvs$m$conf$prescreen[["s2n"]]
@@ -1191,7 +1199,8 @@ mk_shinyscreen_server <- function(projects,init) {
if (rv_presc_flag()) {
shinymsg("Prescreening started. Please wait.")
rv_presc_flag(F)
- m = run(m=rvs$m,phases="prescreen")
+ ## If user changed prescreening params.
+ rvs$m = run(m=rvs$m,phases="prescreen")
rvs$status$is_qa_stat = "Yes."
shinymsg("Prescreening has been completed.")
}
@@ -1634,7 +1643,7 @@ mk_shinyscreen_server <- function(projects,init) {
req(rvs$status$s2n_stat)
})
- output$ret_time_shift_tol = renderText({
+ output$ret_time_shift_tol_stat = renderText({
req(rvs$status$ret_time_shift_tol_stat)
})