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Remove File interaction in VerR #10

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Merged
leopoldguyot merged 1 commit into from
Sep 24, 2025
Merged

Remove File interaction in VerR #10

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127 changes: 2 additions & 125 deletions R/shinyEnvironmentTab.R
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,6 @@
#' @noRd
.createEnvironmentTabUI <- function(id) {
ns <- NS(id)

fluidRow(
id = ns("env_tab"),
column(
Expand Down Expand Up @@ -51,7 +50,7 @@
column(
width = 6,
box(
title = "Global Package/File Manager",
title = "Global Package Manager",
status = "primary",
solidHeader = FALSE,
collapsible = FALSE,
Expand All @@ -67,17 +66,6 @@
- bioc::pkg: Bioconductor (e.g., bioc::edgeR)\n
Tip: Use GitHub to install specific Bioconductor versions.")),
actionButton(ns("install_global_pkg"), "Add Package to All Environments", class = "btn-add-custom", width = "100%"),
tags$hr(),
textInput(ns("global_file_subdir"),
tooltipMaker(
"Target Subdirectory",
"Optional: relative path inside each environment to place the file (e.g., 'data/shared')."),
placeholder = "e.g., data/shared"),
fileInput(ns("global_file"), tooltipMaker(
"Upload File",
"Select a file to upload to all environments. It will be placed in the specified subdirectory if given."
)),
actionButton(ns("upload_global_file"), "Upload to All Environments", class = "btn-add-custom", width = "100%")
)
)
)
Expand Down Expand Up @@ -152,27 +140,6 @@ Tip: Use GitHub to install specific Bioconductor versions.")),
)
})

observeEvent(input$upload_global_file, {
req(input$global_file)
withSpinner(
"Uploading file in all environments...",
{tryCatch({
envs <- envList()
subdir <- gsub("^/|/$", "", input$global_file_subdir)
for (env in envs) {
destPath <- buildEnvPath(env, subdir)
fullDest <- file.path(destPath, input$global_file$name)
if (!dir.exists(destPath)) dir.create(destPath, recursive = TRUE)
file.copy(input$global_file$datapath, fullDest)
}
notifySuccess(HTML(paste(icon("check-circle"), "File uploaded to all environments")))
triggers$file <- triggers$file + 1
}, error = function(e) {
notifyError(HTML(paste(icon("times-circle"), "Upload failed:", e$message)))
})}
)
})

listEnv <- reactive({
triggers$global
envList()
Expand Down Expand Up @@ -221,8 +188,7 @@ Tip: Use GitHub to install specific Bioconductor versions.")),
solidHeader = TRUE,
collapsible = TRUE,
fluidRow(
column(width = 6, packageManagerUI(NS(id, "pkg"))),
column(width = 6, fileManagerUI(NS(id, "file")))
column(width = 12, packageManagerUI(NS(id, "pkg"))),
),
fluidRow(
column(
Expand Down Expand Up @@ -261,7 +227,6 @@ Tip: Use GitHub to install specific Bioconductor versions.")),

# Mount submodules
packageManagerServer("pkg", envName, globalTriggers)
fileManagerServer("file", envName, globalTriggers)

# Delete Environment
observeEvent(input$deleteEnvBtn, {
Expand Down Expand Up @@ -394,91 +359,3 @@ packageManagerServer <- function(id, envName, triggers) {
})
})
}

##########################################
########## File Manager Module ###########
##########################################

#' Create UI for the File Manager Section
#'
#' This function creates the UI elements for file upload and display
#' within an environment box in the VerR Shiny application.
#'
#' @param id A `character(1)` string representing the namespace ID for this UI module.
#'
#' @return A Shiny `box` UI element for file management.
#' @importFrom shiny NS textInput fileInput actionButton
#' @importFrom htmltools strong div tags
#' @importFrom shinydashboard box
#' @importFrom shinyTree shinyTree
#' @noRd
fileManagerUI <- function(id) {
ns <- NS(id)
box(
title = "File Manager",
status = "info",
solidHeader = TRUE,
collapsible = TRUE,
width = 12,
div(
textInput(ns("targetSubdir"), tooltipMaker(
"Target Subdirectory",
"Optional: relative path inside the environment to place the file (e.g., 'data/raw')."),
placeholder = "e.g., data/raw"),
fileInput(ns("addFileInput"), tooltipMaker(
"Upload File",
"Select a file to upload to the environment. It will be placed in the specified subdirectory if given."
)),
actionButton(ns("addFileBtn"), "Add File", class = "btn-add-custom", width = "100%")
),
tags$hr(),
tags$h5(strong("File Tree:")),
shinyTree::shinyTree(ns("treeDisplay"), search = TRUE, theme = "proton")
)
}

#' Server Logic for the File Manager Section
#'
#' This function defines the server-side logic for the file manager module,
#' including handling file uploads and rendering the file tree.
#'
#' @param id A `character(1)` string representing the namespace ID for the module.
#' @param envName A `character(1)` string specifying the name of the environment.
#' @param triggers A `reactiveValues` object containing reactive triggers for file and global updates.
#'
#' @return A Shiny module server function.
#' @importFrom shiny moduleServer observeEvent req icon
#' @importFrom shinyTree renderTree
#' @importFrom htmltools HTML
#' @noRd
fileManagerServer <- function(id, envName, triggers) {
moduleServer(id, function(input, output, session) {
ns <- session$ns

observeEvent(input$addFileBtn, {
req(input$addFileInput)
subdir <- gsub("^/|/$", "", input$targetSubdir)
destPath <- buildEnvPath(envName, subdir)
fullDest <- file.path(destPath, input$addFileInput$name)

withSpinner(
paste0("Uploading file to ", fullDest),
{tryCatch(
{
if (!dir.exists(destPath)) dir.create(destPath, recursive = TRUE)
file.copy(input$addFileInput$datapath, fullDest)
notifySuccess(HTML(paste(icon("check-circle"), "Uploaded:", file.path(subdir, input$addFileInput$name))))
triggers$file <- triggers$file + 1
},
error = function(e) {
notifyError(HTML(paste(icon("times-circle"), "Upload failed:", e$message)))
})}
)
})
output$treeDisplay <- shinyTree::renderTree({
req(envExists(envName))
triggers$file + triggers$global
.getFileTree(buildEnvPath(envName))
})
})
}
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