From 1d41c57611121c3551db1c7739f23fa6af63010f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Fri, 3 Mar 2023 07:54:55 +0100
Subject: [PATCH] Removing some cruft.
---
R/api.R | 41 ----------------------------
R/shiny-state.R | 69 -----------------------------------------------
R/shiny-ui-base.R | 19 -------------
inst/rmd/app.Rmd | 3 +--
4 files changed, 1 insertion(+), 131 deletions(-)
diff --git a/R/api.R b/R/api.R
index 9bc5050..5e90ae1 100644
--- a/R/api.R
+++ b/R/api.R
@@ -273,47 +273,6 @@ mk_comp_tab <- function(m) {
m
}
-
-verify_compounds <- function(conf) {
- ## * Existence of input files
-
- fns_cmpds <- conf$compounds$lists
- fn_cmpd_sets <- conf$compounds$sets
-
- ## ** Compound lists and sets
-
- assert(isThingFile(fn_cmpd_sets),
- msg=paste("Cannot find the compound sets file:",fn_cmpd_sets))
-
- for (fn in fns_cmpds) {
- assert(isThingFile(fn), msg=paste("Cannot find compound list:",fn))
- }
-
- ## * Data files
- df_sets <- file2tab(fn_cmpd_sets)
- all_sets<-unique(df_sets$set)
-
- return(list(conf=conf,all_sets=all_sets))
-}
-
-verify_data_df <- function(data_path,mzml,all_sets) {
- no_file <- which(mzml[,!file.exists(file.path(data_path,file))])
- no_adducts <- which(mzml[,!(adduct %in% names(ADDUCTMAP))])
- no_sets <- which(mzml[,!(set %in% all_sets)])
- assert(length(no_file)==0,msg = paste("Non-existent data files at rows:",paste(no_file,collapse = ',')))
- assert(length(no_adducts)==0,msg = paste("Unrecognised adducts at rows:",paste(no_adducts,collapse = ',')))
- assert(length(no_sets)==0,msg = paste("Unknown sets at rows:",paste(no_sets,collapse = ',')))
-}
-
-verify_data <- function(conf,run,all_sets) {
- ## * Existence of input files
- fn_data <- run$paths$datatab
- assert(isThingFile(fn_data),msg=paste("Data table does not exist:",fn_data))
- mzml <- file2tab(fn_data)
- verify_data_df(run$paths$data,mzml=mzml,all_sets)
- return(conf)
-}
-
#' @export
concurrency <- function(m) {
## Reads the concurrency entry in the config. It is optional, if
diff --git a/R/shiny-state.R b/R/shiny-state.R
index 6759ecd..3450504 100644
--- a/R/shiny-state.R
+++ b/R/shiny-state.R
@@ -482,75 +482,6 @@ gui2datatab <- function(gui) {
}
-pre_extr_val_block <- function(m) {
- if (NROW(m$input$tab$cmpds)==0L) {
- shinymsg("Compound table is still missing.",type="error")
- return(F)
- }
-
- if (NROW(m$input$tab$setid)==0L) {
- shinymsg("Set table is still missing.",type="error")
- return(F)
- }
-
- if (NROW(m$input$tab$mzml)==0L) {
- shinymsg("Table `datatab' is missing.",type="error")
- return(F)
- }
-
- xx <- m$input$tab$mzml
- if (any(is.na(xx$tag))) {
- shinymsg("Some `tag' entries in `datatab' have not been specified.",type='error')
- return(F)
- }
-
- if (any(is.na(xx$adduct))) {
- shinymsg("Some `adduct' entries in `datatab' have not been specified.",type='error')
- return(F)
- }
-
- if (any(is.na(xx$set))) {
- shinymsg("Some `set' entries in `datatab' have not been specified.",type='error')
- return(F)
- }
-
- return(T)
-}
-
-pre_setup_val_block <- function(gui) {
-
- if (!isTruthy(gui$project)) {
- shinymsg("No project yet.", type="error")
- return(F)
- }
-
- if (!isTruthy(head(gui$datatab$file,1))) {
- shinymsg("No data files have been specified yet.", type="error")
- return(F)
- }
-
- if (!isTruthy(all(!is.na(gui$datatab$tag)))) {
- shinymsg("Some tags in datatab are undefined.")
- return(F)
- }
-
- if (!isTruthy(all(!is.na(gui$datatab$tag)))) {
- shinymsg("Some tags in datatab are undefined.")
- return(F)
- }
-
- if (!isTruthy(all(!is.na(gui$datatab$adduct)))) {
- shinymsg("Some adducts in datatab are undefined.")
- return(F)
- }
-
- if (!isTruthy(all(!is.na(gui$datatab$set)))) {
- shinymsg("Some sets in datatab are undefined.")
- return(F)
- }
- T
-}
-
## SHINY HELPERS: COMPOUND INDEX
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index fb719c6..94ec08a 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -22,13 +22,6 @@ obsrv = shiny::observe
obsrv_e = shiny::observeEvent
isol = shiny::isolate
-
-
-embed_rmd <- function(fn) {
-}
-
-
-
celledit_values <- function(col,values,labels=NULL,addna=T) {
if (is.null(labels)) labels = values
if (length(values)==0 || nchar(values)==0) return(character(0))
@@ -917,11 +910,6 @@ mk_shinyscreen_server <- function(projects,init) {
choices = list.files(path=top_data_dir,
pattern = CMPD_LIST_PATT))
- updateSelectInput(session = session,
- inputId = "set_list",
- choices = list.files(path=top_data_dir,
- pattern = SET_LIST_PATT))
-
updateSelectInput(session = session,
inputId = "dfile_list",
choices = list.files(path=top_data_dir,
@@ -1050,13 +1038,6 @@ mk_shinyscreen_server <- function(projects,init) {
message("(config) Selected compound lists: ", paste(sels,collapse = ","))
})
- observeEvent(input$set_list_b, {
- sels = input$set_list
- req(isTruthy(sels))
- message("(config) Selected set lists: ", paste(sels,collapse = ","))
- rvs$gui$compounds$sets = sels
- })
-
observeEvent(rf_get_sets(),{
sets = rf_get_sets()
if (isTruthy(rf_get_sets())) {
diff --git a/inst/rmd/app.Rmd b/inst/rmd/app.Rmd
index 7536ec3..3dd6833 100644
--- a/inst/rmd/app.Rmd
+++ b/inst/rmd/app.Rmd
@@ -34,8 +34,7 @@ def_summ_subset <- shinyscreen:::dtable("QA Column"=shinyscreen:::QA_FLAGS,
validate <- shiny::validate
### def_state$input$tab$tags <- def_datatab
rv_state <- list2rev(def_state)
-compl_sets <- eventReactive(rv_state$input$tab$setid,
- rv_state$input$tab$setid[,unique(set)])
+
### Reactive values to support some of the UI elements.
### rv_ui <- reactiveValues(datatab=def_tags)
--
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