From a0a6c82669582a0192c043bdff66887e742c6420 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Mon, 31 Oct 2022 12:24:11 +0100
Subject: [PATCH] Team meeting changes: made some terminology more accessible
---
R/api.R | 38 +++++++++++++++++++-------------------
R/shiny-ui-base.R | 38 +++++++++++++++++++-------------------
R/state.R | 4 ++--
inst/rmd/app.Rmd | 14 +++++++-------
4 files changed, 47 insertions(+), 47 deletions(-)
diff --git a/R/api.R b/R/api.R
index 3805113..65d7014 100644
--- a/R/api.R
+++ b/R/api.R
@@ -700,22 +700,22 @@ create_plots <- function(m) {
#' `rmarkdown::run` `shiny_args` argument.
#' @param render_args `list`, optional list of arguments conveyed to
#' `rmarkdown::run` `render_args` argument.
-#' @param indir `character(1)`, a location on the server side
+#' @param top_data_dir `character(1)`, a location on the server side
#' containing data directories.
-#' @param userdir `character(1)`, a location on the server side containing project directories.
+#' @param projects `character(1)`, a location on the server side containing project directories.
#' @return Nada.
#' @author Todor Kondić
-app <- function(shiny_args=list(launch.browser=F),render_args=NULL,indir=getwd(),userdir=getwd()) {
+app <- function(shiny_args=list(launch.browser=F),render_args=NULL,top_data_dir=getwd(),projects=getwd()) {
dir_before <- getwd()
init <- list()
init$dir_before <- dir_before
- init$indir <- norm_path(indir)
- init$userdir <- norm_path(userdir)
- if (!dir.exists(init$indir)) stop("Data directory (indir), currently `",
- init$indir,
+ init$top_data_dir <- norm_path(top_data_dir)
+ init$projects <- norm_path(projects)
+ if (!dir.exists(init$top_data_dir)) stop("Data directory (top_data_dir), currently `",
+ init$top_data_dir,
"` does not exist. Abort.")
- if (!dir.exists(init$userdir)) stop("User root directory (userdir), currently `",
- init$userdir,"` does not exist.. Abort.")
+ if (!dir.exists(init$projects)) stop("User root directory (projects), currently `",
+ init$projects,"` does not exist.. Abort.")
on.exit(expr=setwd(dir_before))
dir_start <- tempfile("shinyscreen")
@@ -731,27 +731,27 @@ app <- function(shiny_args=list(launch.browser=F),render_args=NULL,indir=getwd()
#' @export
#' @title serve
-#' @param indir `character(1)`, a location on the server side
+#' @param top_data_dir `character(1)`, a location on the server side
#' containing data directories.
-#' @param topuserdir `character(1)`, a location on the server side
+#' @param usersdir `character(1)`, a location on the server side
#' containing individual user directories.
-#' @param user `character(1)`, subdir of topuserdir.
+#' @param user `character(1)`, subdir of usersdir.
#' @param host `character(1)`, optional, address where the page is
#' served.
#' @param port `integer(1)`, optional, port at which the page is
#' served.
#' @return Nada.
#' @author Todor Kondić
-serve <- function(indir,topuserdir,user,host='0.0.0.0',port=7777) {
+serve <- function(top_data_dir,usersdir,user,host='0.0.0.0',port=7777) {
shiny_args <- c(list(launch.browser=F),list(host=host,port=port))
- userdir <- file.path(topuserdir,user)
- if (!dir.exists(userdir)) {
- dir.create(userdir)
- message('Created userdir: ',userdir)
+ projects <- file.path(usersdir,user)
+ if (!dir.exists(projects)) {
+ dir.create(projects)
+ message('Created projects: ',projects)
} else {
- message('Using existing userdir: ', userdir)
+ message('Using existing projects: ', projects)
}
- app(shiny_args=shiny_args,indir=indir,userdir=userdir)
+ app(shiny_args=shiny_args,top_data_dir=top_data_dir,projects=projects)
}
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index f9d3d54..c730e22 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -929,51 +929,51 @@ mk_shinyscreen_server <- function(projects,init) {
## OBSERVERS: PROJECT MANAGEMENT
observe({
- indir <- rvs$gui$paths$project
- req(isTruthy(indir) && dir.exists(indir))
+ top_data_dir <- rvs$gui$paths$project
+ req(isTruthy(top_data_dir) && dir.exists(top_data_dir))
updateSelectInput(session = session,
inputId = "comp_list",
- choices = list.files(path=indir,
+ choices = list.files(path=top_data_dir,
pattern = CMPD_LIST_PATT))
updateSelectInput(session = session,
inputId = "set_list",
- choices = list.files(path=indir,
+ choices = list.files(path=top_data_dir,
pattern = SET_LIST_PATT))
updateSelectInput(session = session,
inputId = "dfile_list",
- choices = list.files(path=indir,
+ choices = list.files(path=top_data_dir,
pattern = DFILES_LIST_PATT))
updateSelectInput(session = session,
- inputId = "indir_list",
- selected = basename(indir),
- choices = list.dirs(path = init$indir,
+ inputId = "top_data_dir_list",
+ selected = basename(top_data_dir),
+ choices = list.dirs(path = init$top_data_dir,
full.names = F,
recursive = F))
})
observe({
- indir <- rvs$gui$paths$data
- req(isTruthy(indir) && dir.exists(indir))
+ top_data_dir <- rvs$gui$paths$data
+ req(isTruthy(top_data_dir) && dir.exists(top_data_dir))
updateSelectInput(session = session,
inputId = "dfile_list",
- choices = list.files(path=indir,
+ choices = list.files(path=top_data_dir,
pattern = DFILES_LIST_PATT))
})
## Update projects and data directories every second.
observeEvent(rtimer1000(),{
projects <- rv_projects()
- curr_projects <- list.dirs(path=init$userdir, full.names = F, recursive = F)
+ curr_projects <- list.dirs(path=init$projects, full.names = F, recursive = F)
if (length(union(curr_projects,projects)) != length(intersect(curr_projects,projects))) {
updateSelectInput(session=session,
inputId="proj_list",
choices=curr_projects)
updateSelectInput(session=session,
- inputId="indir_list",
+ inputId="top_data_dir_list",
choices=curr_projects)
rv_projects(curr_projects)
}
@@ -986,7 +986,7 @@ mk_shinyscreen_server <- function(projects,init) {
## loaded. Everything else works off rvs$m and rvs$gui.
wd <- input$proj_list
req(!is.null(wd) && !is.na(wd) && nchar(wd)>0)
- fullwd <- file.path(init$userdir,wd)
+ fullwd <- file.path(init$projects,wd)
fullwdq <- file.exists(fullwd)
if (!fullwdq) {
stop("The project path does not exist!?")
@@ -999,7 +999,7 @@ mk_shinyscreen_server <- function(projects,init) {
pack <- readRDS(file=fn_packed_state)
rvs$gui <- unpack_app_state(session=session,
input=input,
- top_data_dir=init$indir,
+ top_data_dir=init$top_data_dir,
project_path=fullwd,
packed_state=pack)
## Load computational state.
@@ -1052,10 +1052,10 @@ mk_shinyscreen_server <- function(projects,init) {
shinymsg("Saving state completed.")
})
- observeEvent(input$sel_indir_b,{
- indir <- input$indir_list
- req(isTruthy(indir))
- rvs$gui$paths$data <- file.path(init$indir, indir)
+ observeEvent(input$sel_data_dir_b,{
+ data_dir <- input$top_data_dir_list
+ req(isTruthy(data_dir))
+ rvs$gui$paths$data <- file.path(init$top_data_dir, data_dir)
message("Selected data dir:",rvs$gui$paths$data)
diff --git a/R/state.R b/R/state.R
index 5bfb605..319cb10 100644
--- a/R/state.R
+++ b/R/state.R
@@ -40,7 +40,7 @@ runtime_from_conf <- function(run,conf) {
run
}
-reinit_run_data <- function(userdir,top_data_dir,project,run=NULL) {
+reinit_run_data <- function(projects,top_data_dir,project,run=NULL) {
if (!is.null(run)) {
olddata <- run$paths$data
oldproject <- basename(run$paths$project)
@@ -51,7 +51,7 @@ reinit_run_data <- function(userdir,top_data_dir,project,run=NULL) {
if (isTruthy(olddata)) run$paths$data <- file.path(top_user_dir,basename(olddata))
}
run$project <- project
- run$paths$project <- file.path(userdir,project)
+ run$paths$project <- file.path(projects,project)
run
}
diff --git a/inst/rmd/app.Rmd b/inst/rmd/app.Rmd
index b263be1..1f09979 100644
--- a/inst/rmd/app.Rmd
+++ b/inst/rmd/app.Rmd
@@ -58,8 +58,8 @@ rv_rtrange <- reactiveValues(min=def_state$conf$rt_min,
rv_mzrange <- reactiveValues(min=NA,
max=NA)
-projects <- list.dirs(path=init$userdir, full.names = F, recursive = F)
-inputdirs <- list.dirs(path=init$indir, full.names = F, recursive = F)
+projects <- list.dirs(path=init$projects, full.names = F, recursive = F)
+inputdirs <- list.dirs(path=init$top_data_dir, full.names = F, recursive = F)
```
<style type="text/css">
@@ -78,7 +78,7 @@ inputdirs <- list.dirs(path=init$indir, full.names = F, recursive = F)
<summary>Projects, input directories and compound lists</summary>
When you start the program with `app` function, you define two
-superdirecotories: `userdir` and `indir`. Directory `userdir` contains
+superdirectories: `projects` and `top_data_dir`. Directory `projects` contains
all the existing projects and any new projects defined during the
current session will be saved here. Data inside a project directory
consists of intermediate files, saved states and workflow outputs.
@@ -93,7 +93,7 @@ settings and selected inputs.
Each `Shinyscreen` project needs input data: mass spectrometry files
(in mzML format), compound and set lists. These should all be present
before starting `Shinyscreen` in one of the directories under
-`userdir`.
+`projects`.
@@ -157,7 +157,7 @@ downloadButtonRmd("dwn_proj_b",
<details>
<summary>More on data directories</summary>
-Data directory is a subdirectory of the `indir` directory which is
+Data directory is a subdirectory of the `top_data_dir` directory which is
one of the arguments to `app` function used to start Shinyscreen
GUI. It contains the `mzML` data files.
@@ -167,10 +167,10 @@ Select one of the data directories from the list by clicking the
</details>
```{r, echo=F}
-selectInput('indir_list',
+selectInput('top_data_dir_list',
label = "Input directories",
choices = inputdirs)
-actionButton(inputId = "sel_indir_b",
+actionButton(inputId = "sel_data_dir_b",
label= "Select")
textOutput("curr_data_dir")
```
--
GitLab