Generic module server function for saving files that are exported to the Platform
mod_save_file_generic_server.RdServer side of the shiny Module that allows users to save files generated within the Shiny app and export them to the project on the Seven Bridges Platform.
Arguments
- id
Module's ID.
- reac_vals
Reactive values list containing mandatory fields:
`FUN`- Function for creating a file, i.e `write.table`, `save`, `write`, `write_json`, `write_xml`, `SaveH5Seurat` etc.
`args`- List of function arguments for the provided FUN.
`filename`- File name.
`extension`- The expected file extension. Please provide the expected file extension if available, in order to properly validate the existence of the file with the same name and extension.
`overwrite`- Boolean. Overwrite the existing file with the same name.
- sbg_directory_path
Path to the mounted `sbgenomics` directory containing `project-files`, `output-files` and `workspace` sub-directories on the instance. These directories are expected to exist on the instance where the app will run. For the purpose of testing your app locally, you can create a mock directory `sbgenomics` with the same structure - containing sub-directories `project-files`, `output-files` and `workspace` and populate them with test files mimicking the project file structure on the Platform.
Examples
library(shiny)
library(magrittr)
library(sbShinyModules)
library(reactable)
library(jsonlite)
###### Test modules for demonstrating nested modules ######
test_module_ui <- function(id) {
ns <- NS(id)
tagList(
actionButton(
inputId = ns("test_module_btn"),
label = "Test nesting modules",
width = "100%"
)
)
}
test_module_server <- function(id) {
moduleServer(id, module = function(input, output, session) {
ns <- session$ns
observeEvent(input$test_module_btn, {
showModal(
ui = modalDialog(
title = "Test nested modules",
size = "l",
tagList(
reactable::reactableOutput(ns("nested_table_data")),
fluidRow(
column(
width = 6,
sbShinyModules::mod_save_file_generic_ui(ns("save_file_nested"))
)
)
),
footer = tagList(
actionButton(ns("dismiss"),
label = "Dismiss",
icon = icon("xmark")
)
)
)
)
})
output$nested_table_data <- reactable::renderReactable({
reactable::reactable(iris,
onClick = "select",
filterable = TRUE,
searchable = TRUE,
resizable = TRUE,
defaultPageSize = 10
)
})
# Close the modal dialog by clicking the dismiss button
observeEvent(input$dismiss, {
removeModal()
})
# Create the reactive values list with mandatory fields to pass to the
# module
helper_rv_nested <- reactiveValues(
FUN = write.table,
args = list(x = iris, quote = FALSE, row.names = FALSE, col.names = TRUE),
filename = "generic_file_name",
extension = ".txt",
overwrite = TRUE
)
# Call the file exporter module
sbShinyModules::mod_save_file_generic_server(
id = "save_file_nested",
reac_vals = helper_rv_nested,
sbg_directory_path = system.file("demos/sbgenomics_test",
package = "sbShinyModules"
)
)
})
}
############## Test modules end ###########################
##### Demo App UI #######
ui <- fluidPage(
titlePanel("Save data for the export to the Platform - Module Demo"),
sidebarLayout(
sidebarPanel(
fluidRow(
h3("Export txt/csv to the Platform"),
br(),
textInput("file_name", label = "Set file name", width = "100%"),
fluidRow(
column(
width = 6,
selectInput("separator",
label = "Set separator",
choices = c("comma", "tab", "new line", "semicolon")
)
),
column(
width = 6,
selectInput("extension",
label = "Set extension",
choices = c("txt", "csv")
)
)
),
fluidRow(
column(
width = 6,
radioButtons("overwrite",
label = "Overwrite existing file?",
choiceNames = c("yes", "no"),
choiceValues = c("TRUE", "FALSE")
)
)
),
fluidRow(
column(
width = 12,
sbShinyModules::mod_save_file_generic_ui(
id = "file_exporter",
save_button_title = "Save txt/csv"
)
)
)
),
fluidRow(
h3("Export json to the Platform"),
br(),
textInput("file_name_json", label = "Set file name", width = "100%"),
fluidRow(
column(
width = 12,
sbShinyModules::mod_save_file_generic_ui(
id = "json_file_exporter",
save_button_title = "Save json"
)
)
)
),
fluidRow(
h3("Export RDS object to the Platform"),
br(),
textInput("file_name_rds", label = "Set file name", width = "100%"),
fluidRow(
column(
width = 12,
sbShinyModules::mod_save_file_generic_ui(
id = "rds_file_exporter",
save_button_title = "Save RDS"
)
)
)
),
fluidRow(
h3("Test nested modules"),
br(),
fluidRow(
column(
width = 12,
test_module_ui(id = "nested_modules")
)
)
)
),
mainPanel(
reactable::reactableOutput("table_data")
)
)
)
###### Demo App Server Logic ######
server <- function(input, output, session) {
output$table_data <- reactable::renderReactable({
reactable::reactable(iris,
onClick = "select",
filterable = TRUE,
searchable = TRUE,
resizable = TRUE,
defaultPageSize = 10
)
})
# Create the reactive values list with mandatory fields to pass to the module
helper_rv_table <- reactiveValues(
FUN = write.table,
args = list(x = iris, quote = FALSE, row.names = FALSE, col.names = TRUE),
filename = NULL,
extension = NULL,
overwrite = FALSE
)
observe(
helper_rv_table$filename <- as.character(input$file_name)
)
observe(
helper_rv_table$args[["sep"]] <- switch(input$separator,
"comma" = ",",
"tab" = "\t",
"new line" = "\n",
"semicolon" = ";"
)
)
observe(
helper_rv_table$extension <- as.character(input$extension)
)
observe(
helper_rv_table$overwrite <- as.logical(input$overwrite)
)
# Call the file exporter module
sbShinyModules::mod_save_file_generic_server(
id = "file_exporter",
reac_vals = helper_rv_table,
sbg_directory_path = system.file("demos/sbgenomics_test",
package = "sbShinyModules"
)
)
# Create reactive values list for the json file export
helper_rv_json <- reactiveValues(
FUN = write,
args = list(
x = jsonlite::toJSON(x = iris, dataframe = "rows", pretty = TRUE)
),
filename = NULL,
extension = "json",
overwrite = TRUE
)
observe(
helper_rv_json$filename <- as.character(input$file_name_json)
)
# Call the file exporter module
sbShinyModules::mod_save_file_generic_server(
id = "json_file_exporter",
reac_vals = helper_rv_json,
sbg_directory_path = system.file("demos/sbgenomics_test",
package = "sbShinyModules"
)
)
# Create reactive values list for the RDS file export
helper_rv_rds <- reactiveValues(
FUN = saveRDS,
args = list(
object = iris
),
filename = NULL,
extension = "RDS",
overwrite = TRUE
)
observe(
helper_rv_rds$filename <- as.character(input$file_name_rds)
)
# Call the file exporter module
sbShinyModules::mod_save_file_generic_server(
id = "rds_file_exporter",
reac_vals = helper_rv_rds,
sbg_directory_path = system.file("demos/sbgenomics_test",
package = "sbShinyModules"
)
)
# Note: This way the file will be saved in a specific directory within the
# package installation path. To find this default location, you can use the
# following R command to determine the installation path of the
# sbShinyModules package:
#
# find.package("sbShinyModules")
#
# Within this directory, exported files will be placed under:
#
# demos/sbgenomics_test/output-files
#
# You can specify your own destination directory for exported files by
# setting the sbg_directory_path parameter in the
# mod_save_file_generic_server() function. Ensure that the custom directory
# you choose follows the required organizational structure for proper
# functionality. Refer to the sbg_directory_path parameter description in the
# documentation for detailed requirements.
# Call the test module
test_module_server(id = "nested_modules")
}
###### Run the Shiny app #######
shinyApp(ui, server)