From ec102c7a515950cdf0deda1c8afe8b52f8d177c7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Fri, 1 Jul 2022 17:20:43 +0200
Subject: [PATCH] ...
---
R/shiny-state.R | 21 ++++++++++++++++----
R/shiny-ui-base.R | 49 ++++++++++++++++++++++++++++++-----------------
2 files changed, 48 insertions(+), 22 deletions(-)
diff --git a/R/shiny-state.R b/R/shiny-state.R
index fb632a7..b84ca71 100644
--- a/R/shiny-state.R
+++ b/R/shiny-state.R
@@ -33,7 +33,7 @@ create_stub_gui <- function() {
gui <- list()
shiny::isolate({
gui$compounds <- shiny::reactiveValues(lists=character(),
- set=character())
+ sets=character())
gui$datatab <- shiny::reactiveValues(file=character(),
tag=character(),
adduct=character(),
@@ -83,10 +83,10 @@ r2taadse <- function(tablist,sets) {
r2compounds <- function(rcompounds) {
shiny::isolate({
cmpd_lists <- rcompounds$lists
- cmpd_set <- rcompounds$set
+ cmpd_set <- rcompounds$sets
})
- list(lists=cmpd_lists,set=cmpd_set)
+ list(lists=cmpd_lists,sets=cmpd_set)
}
@@ -211,9 +211,22 @@ app_state2state <- function(input,gui) {
m <- new_project(gui$paths$project)
m$run$paths <- shiny::reactiveValuesToList(gui$paths)
m$conf <- input2conf(input)
+ m$input$tab$mzml <- data.table(tag=gui$datatab$tag,
+ adduct=gui$datatab$adduct,
+ set=gui$datatab$set,
+ file=gui$datatab$file)
m
}
-
+gen_comp_state <- function(input,gui) {
+ m <- app_state2state(input,gui)
+ run(m=m,phases=c("setup","mk_comp_tab"))
+}
+
+get_sets <- function(gui) {
+ fn_set <- file.path(gui$paths$project,gui$compounds$sets)
+ df <- fread(file=fn_sets)
+ df[,unique(set)]
+}
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index 790daf9..c716ac2 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -439,7 +439,7 @@ mk_shinyscreen_server <- function(projects,init) {
## Update with data-files.
rv_dfile <- reactiveVal(def_datafiles)
-
+ ## TODO: think about the connection of rv_dfile to the rest.
## Data-file table when loading.
rv_datatab <- reactiveVal(def_datatab)
rv_flag_datatab <- reactiveVal(-.Machine$integer.max)
@@ -654,24 +654,37 @@ mk_shinyscreen_server <- function(projects,init) {
## REACTIVE FUNCTIONS
- rf_compound_input_state <- reactive({
- sets <- rvs$m$run$paths$compounds$sets
- lst <- as.list(rvs$m$run$paths$compounds$lists)
- ## TODO XXX
- validate(need(length(lst)>0,
- message = "Load the compound lists(s) first."))
- validate(need(length(sets)>0 && nchar(sets)>0,
- message = "Load the setid table first."))
- isolate({
- state <- rev2list(rvs$m)
- m <- load_compound_input(state)
-
- ## Side effect! This is because my pipeline logic does not
- ## work nicely with reactive stuff.
- rvs$m$input$tab$cmpds <- list2rev(m$input$tab$cmpds)
- rvs$m$input$tab$setid <- m$input$tab$setid
- m
+ ## rf_compound_input_state <- reactive({
+ ## sets <- rvs$m$run$paths$compounds$sets
+ ## lst <- as.list(rvs$m$run$paths$compounds$lists)
+ ## ## TODO XXX
+ ## validate(need(length(lst)>0,
+ ## message = "Load the compound lists(s) first."))
+ ## validate(need(length(sets)>0 && nchar(sets)>0,
+ ## message = "Load the setid table first."))
+ ## isolate({
+ ## state <- rev2list(rvs$m)
+ ## m <- load_compound_input(state)
+
+ ## ## Side effect! This is because my pipeline logic does not
+ ## ## work nicely with reactive stuff.
+ ## rvs$m$input$tab$cmpds <- list2rev(m$input$tab$cmpds)
+ ## rvs$m$input$tab$setid <- m$input$tab$setid
+ ## m
+ ## })
+ ## })
+
+ rf_comp_state <- reactive({
+ app_state2state(input=input,
+ gui = rvs$gui)
})
+
+ rf_get_sets <- reactive({
+ req(rvs$gui$paths$project)
+ req(rvs$gui$paths$sets)
+
+ get_sets(gui)
+
})
rf_conf_proj <- reactive({
--
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