mirror of
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435 lines
12 KiB
R
435 lines
12 KiB
R
#' Shiny module to browser and export REDCap data
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#'
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#' @param id Namespace id
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#' @param include_title logical to include title
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#'
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#' @rdname redcap_read_shiny_module
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#'
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#' @return shiny ui element
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#' @export
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m_redcap_readUI <- function(id, include_title = TRUE) {
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ns <- shiny::NS(id)
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server_ui <- shiny::tagList(
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# width = 6,
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shiny::tags$h4("REDCap server"),
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shiny::textInput(
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inputId = ns("uri"),
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label = "Web address",
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value = "https://redcap.your.institution/"
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),
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shiny::helpText("Format should be either 'https://redcap.your.institution/' or 'https://your.institution/redcap/'"),
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shiny::textInput(
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inputId = ns("api"),
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label = "API token",
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value = ""
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),
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shiny::helpText("The token is a string of 32 numbers and letters."),
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shiny::actionButton(
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inputId = ns("data_connect"),
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label = "Connect",
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icon = shiny::icon("link", lib = "glyphicon"),
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# width = NULL,
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disabled = TRUE
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),
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shiny::br(),
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shiny::br(),
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tags$div(
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id = ns("connect-placeholder"),
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shinyWidgets::alert(
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id = ns("connect-result"),
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status = "info",
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tags$p(phosphoricons::ph("info", weight = "bold"), "Please fill in server address (URI) and API token, then press 'Connect'.")
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),
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dismissible = TRUE
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),
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shiny::br()
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)
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params_ui <-
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shiny::tagList(
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# width = 6,
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shiny::tags$h4("Data import parameters"),
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shiny::helpText("Options here will show, when API and uri are typed"),
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shiny::uiOutput(outputId = ns("fields")),
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shinyWidgets::switchInput(
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inputId = "do_filter",
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label = "Apply filter?",
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value = FALSE,
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inline = FALSE,
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onLabel = "YES",
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offLabel = "NO"
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),
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shiny::conditionalPanel(
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condition = "input.do_filter",
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shiny::uiOutput(outputId = ns("arms")),
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shiny::textInput(
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inputId = ns("filter"),
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label = "Optional filter logic (e.g., [gender] = 'female')"
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)
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)
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)
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shiny::fluidPage(
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if (include_title) shiny::tags$h3("Import data from REDCap"),
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bslib::layout_columns(
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server_ui,
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params_ui,
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col_widths = bslib::breakpoints(
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sm = c(12, 12),
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md = c(12, 12)
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)
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),
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shiny::column(
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width = 12,
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# shiny::actionButton(inputId = ns("import"), label = "Import"),
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## TODO: Use busy indicator like on download to have button activate/deactivate
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shiny::actionButton(
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inputId = ns("data_import"),
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label = "Import",
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icon = shiny::icon("download", lib = "glyphicon"),
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width = "100%",
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disabled = TRUE
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),
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# bslib::input_task_button(
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# id = ns("data_import"),
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# label = "Import",
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# icon = shiny::icon("download", lib = "glyphicon"),
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# label_busy = "Just a minute...",
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# icon_busy = fontawesome::fa_i("arrows-rotate",
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# class = "fa-spin",
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# "aria-hidden" = "true"
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# ),
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# type = "primary",
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# auto_reset = TRUE#,state="busy"
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# ),
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shiny::br(),
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shiny::br(),
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shiny::helpText("Press 'Import' to get data from the REDCap server. Check the preview below before proceeding."),
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shiny::br(),
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shiny::br()
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)
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)
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}
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#' @rdname redcap_read_shiny_module
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#'
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#' @return shiny server module
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#' @export
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#'
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m_redcap_readServer <- function(id) {
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module <- function(input, output, session) {
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ns <- session$ns
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data_rv <- shiny::reactiveValues(
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dd_status = NULL,
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data_status = NULL,
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uri = NULL,
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project_name = NULL,
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info = NULL,
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arms = NULL,
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dd_list = NULL,
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data = NULL
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)
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shiny::observeEvent(list(input$api, input$uri), {
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uri <- paste0(ifelse(endsWith(input$uri, "/"), input$uri, paste0(input$uri, "/")), "api/")
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if (is_valid_redcap_url(uri) & is_valid_token(input$api)) {
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data_rv$uri <- uri
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shiny::updateActionButton(inputId = "data_connect", disabled = FALSE)
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} else {
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shiny::updateActionButton(inputId = "data_connect", disabled = TRUE)
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}
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})
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tryCatch(
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{
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shiny::observeEvent(
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list(
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input$data_connect
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),
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{
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shiny::req(input$api)
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shiny::req(data_rv$uri)
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parameters <- list(
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redcap_uri = data_rv$uri,
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token = input$api
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)
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# browser()
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imported <- try(rlang::exec(REDCapR::redcap_metadata_read, !!!parameters), silent = TRUE)
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## TODO: Simplify error messages
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if (inherits(imported, "try-error") || NROW(imported) < 1 || ifelse(is.list(imported), !isTRUE(imported$success), FALSE)) {
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if (ifelse(is.list(imported), !isTRUE(imported$success), FALSE)) {
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mssg <- imported$raw_text
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} else {
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mssg <- attr(imported, "condition")$message
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}
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datamods:::insert_error(mssg = mssg, selector = "connect")
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data_rv$dd_status <- "error"
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data_rv$dd_list <- NULL
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} else if (isTRUE(imported$success)) {
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data_rv$dd_status <- "success"
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data_rv$project_name <- REDCapR::redcap_project_info_read(
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redcap_uri = data_rv$uri,
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token = input$api
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)$data$project_title
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datamods:::insert_alert(
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selector = ns("connect"),
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status = "success",
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include_data_alert(
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dataIdName = "see_data",
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extra = tags$p(tags$b(phosphoricons::ph("check", weight = "bold"), "Connected to server!"), tags$p(paste0(data_rv$project_name, " loaded."))),
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btn_show_data = TRUE
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)
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)
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data_rv$dd_list <- imported
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}
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},
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ignoreInit = TRUE
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)
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},
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warning = function(warn) {
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showNotification(paste0(warn), type = "warning")
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},
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error = function(err) {
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showNotification(paste0(err), type = "err")
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}
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)
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shiny::observeEvent(input$see_data, {
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datamods::show_data(
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purrr::pluck(data_rv$dd_list, "data"),
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title = "Data dictionary",
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type = "modal",
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show_classes = FALSE,
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tags$b("Preview:")
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)
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})
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arms <- shiny::reactive({
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shiny::req(input$api)
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shiny::req(data_rv$uri)
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REDCapR::redcap_event_read(
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redcap_uri = data_rv$uri,
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token = input$api
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)$data
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})
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output$fields <- shiny::renderUI({
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shiny::req(data_rv$dd_list)
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shinyWidgets::virtualSelectInput(
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inputId = ns("fields"),
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label = "Select variables to import:",
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choices = purrr::pluck(data_rv$dd_list, "data") |>
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dplyr::select(field_name, form_name) |>
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(\(.x){
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split(.x$field_name, .x$form_name)
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})(),
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updateOn = "change",
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multiple = TRUE,
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search = TRUE,
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showValueAsTags = TRUE
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)
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})
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shiny::observeEvent(input$fields, {
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if (is.null(input$fields) | length(input$fields) == 0) {
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shiny::updateActionButton(inputId = "data_import", disabled = TRUE)
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} else {
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shiny::updateActionButton(inputId = "data_import", disabled = FALSE)
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}
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})
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output$arms <- shiny::renderUI({
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vectorSelectInput(
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inputId = ns("arms"),
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selected = NULL,
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label = "Filter by events/arms",
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data = stats::setNames(arms()[[3]],arms()[[1]]),
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multiple = TRUE
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)
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})
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shiny::observeEvent(input$data_import, {
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shiny::req(input$fields)
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record_id <- purrr::pluck(data_rv$dd_list, "data")[[1]][1]
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parameters <- list(
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uri = data_rv$uri,
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token = input$api,
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fields = unique(c(record_id, input$fields)),
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events = input$arms,
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raw_or_label = "both",
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filter_logic = input$filter
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)
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shiny::withProgress(message = "Downloading REDCap data. Hold on for a moment..", {
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imported <- try(rlang::exec(REDCapCAST::read_redcap_tables, !!!parameters), silent = TRUE)
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})
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code <- rlang::call2(REDCapCAST::read_redcap_tables, !!!parameters)
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if (inherits(imported, "try-error") || NROW(imported) < 1) {
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data_rv$data_status <- "error"
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data_rv$data_list <- NULL
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} else {
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data_rv$data_status <- "success"
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data_rv$data <- imported |>
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REDCapCAST::redcap_wider() |>
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dplyr::select(-dplyr::ends_with("_complete")) |>
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dplyr::select(-dplyr::any_of(record_id)) |>
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REDCapCAST::suffix2label()
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}
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})
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return(shiny::reactive(data_rv$data))
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}
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shiny::moduleServer(
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id = id,
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module = module
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)
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}
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#' @importFrom htmltools tagList tags
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#' @importFrom shiny icon getDefaultReactiveDomain
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include_data_alert <- function(dataIdName = "see_data",
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btn_show_data,
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see_data_text = "Click to see data",
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extra = NULL,
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session = shiny::getDefaultReactiveDomain()) {
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if (isTRUE(btn_show_data)) {
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success_message <- tagList(
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extra,
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tags$br(),
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shiny::actionLink(
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inputId = session$ns(dataIdName),
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label = tagList(phosphoricons::ph("table"), see_data_text)
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)
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)
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}
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return(success_message)
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}
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# #' REDCap import teal data module
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# #'
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# #' @rdname redcap_read_shiny_module
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# tdm_redcap_read <- teal::teal_data_module(
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# ui <- function(id) {
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# shiny::fluidPage(
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# m_redcap_readUI(id)
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# )
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# },
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# server = function(id) {
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# m_redcap_readServer(id, output.format = "teal")
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# }
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# )
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#' Title
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#'
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#' @param url
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#'
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#' @returns
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#' @export
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#'
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#' @examples
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#' url <- c(
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#' "www.example.com",
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#' "http://example.com",
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#' "https://redcap.your.inst/api/"
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#' )
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#' is_valid_redcap_url(url)
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is_valid_redcap_url <- function(url) {
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pattern <- "https://[^ /$.?#].[^\\s]*/api/$"
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stringr::str_detect(url, pattern)
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}
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#' Validate REDCap token
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#'
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#' @param token token
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#' @param pattern_env pattern
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#'
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#' @returns
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#' @export
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#'
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#' @examples
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#' token <- paste(sample(c(1:9, LETTERS[1:6]), 32, TRUE), collapse = "")
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#' is_valid_token(token)
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is_valid_token <- function(token, pattern_env = NULL, nchar = 32) {
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checkmate::assert_character(token, any.missing = TRUE, len = 1)
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if (!is.null(pattern_env)) {
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checkmate::assert_character(pattern_env,
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any.missing = FALSE,
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len = 1
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)
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pattern <- pattern_env
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} else {
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pattern <- glue::glue("^([0-9A-Fa-f]{<nchar>})(?:\\n)?$",
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.open = "<",
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.close = ">"
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)
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}
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if (is.na(token)) {
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out <- FALSE
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} else if (is.null(token)) {
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out <- FALSE
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} else if (nchar(token) == 0L) {
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out <- FALSE
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} else if (!grepl(pattern, token, perl = TRUE)) {
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out <- FALSE
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} else {
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out <- TRUE
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}
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out
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}
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#' Test app for the redcap_read_shiny_module
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#'
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#' @rdname redcap_read_shiny_module
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#'
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#' @examples
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#' \dontrun{
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#' redcap_demo_app()
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#' }
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redcap_demo_app <- function() {
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ui <- shiny::fluidPage(
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m_redcap_readUI("data"),
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toastui::datagridOutput2(outputId = "redcap_prev"),
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DT::DTOutput("data_summary")
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)
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server <- function(input, output, session) {
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data_val <- shiny::reactiveValues(data = NULL)
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data_val$data <- m_redcap_readServer(id = "data")
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output$data_summary <- DT::renderDataTable(
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{
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shiny::req(data_val$data)
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data_val$data()
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},
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options = list(
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scrollX = TRUE,
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pageLength = 5
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),
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)
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}
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shiny::shinyApp(ui, server)
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}
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