mirror of
https://github.com/agdamsbo/FreesearchR.git
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696 lines
20 KiB
R
696 lines
20 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, title = TRUE, url = NULL) {
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ns <- shiny::NS(id)
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if (isTRUE(title)) {
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title <- shiny::tags$h4(i18n$t("Import data from REDCap"), class = "redcap-module-title")
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}
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server_ui <- shiny::tagList(
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shiny::tags$h4(i18n$t("REDCap server")),
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shiny::textInput(
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inputId = ns("uri"),
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label = i18n$t("Web address"),
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value = if_not_missing(url, "https://redcap.your.institution/"),
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width = "100%"
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),
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shiny::helpText(
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i18n$t(
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"Format should be either 'https://redcap.your.institution/' or 'https://your.institution/redcap/'"
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)
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),
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shiny::br(),
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shiny::br(),
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shiny::passwordInput(
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inputId = ns("api"),
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label = i18n$t("API token"),
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value = "",
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width = "100%"
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),
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shiny::helpText(i18n$t(
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"The token is a string of 32 numbers and letters."
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)),
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shiny::br(),
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shiny::br(),
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shiny::actionButton(
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inputId = ns("data_connect"),
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label = i18n$t("Connect"),
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icon = shiny::icon("link", lib = "glyphicon"),
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width = "100%",
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disabled = TRUE
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),
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shiny::br(),
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shiny::br(),
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tags$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$p(
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phosphoricons::ph("info", weight = "bold"),
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i18n$t("Please fill in web address and API token, then press 'Connect'.")
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)
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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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filter_ui <-
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shiny::tagList(
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# width = 6,
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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 = i18n$t("Optional filter logic (e.g., [gender] = 'female')")
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)
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)
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params_ui <-
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shiny::tagList(
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shiny::tags$h4(i18n$t("Data import parameters")),
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shiny::tags$div(
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style = htmltools::css(
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display = "grid",
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gridTemplateColumns = "1fr 50px",
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gridColumnGap = "10px"
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),
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shiny::uiOutput(outputId = ns("fields")),
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shiny::tags$div(
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class = "shiny-input-container",
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shiny::tags$label(
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class = "control-label",
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`for` = ns("dropdown_params"),
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"...",
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style = htmltools::css(visibility = "hidden")
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),
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shinyWidgets::dropMenu(
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shiny::actionButton(
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inputId = ns("dropdown_params"),
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label = shiny::icon("filter"),
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width = "50px"
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),
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filter_ui
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)
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)
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),
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shiny::helpText(
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i18n$t(
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"Select fields/variables to import and click the funnel to apply optional filters"
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)
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),
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shiny::tags$br(),
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shiny::tags$br(),
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shiny::uiOutput(outputId = ns("data_type")),
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shiny::uiOutput(outputId = ns("fill")),
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shiny::actionButton(
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inputId = ns("data_import"),
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label = i18n$t("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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shiny::tags$br(),
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shiny::tags$br(),
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tags$div(
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id = ns("retrieved-placeholder"),
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shinyWidgets::alert(
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id = ns("retrieved-result"),
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status = "info",
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tags$p(
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phosphoricons::ph("info", weight = "bold"),
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"Please specify data to download, then press 'Import'."
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)
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),
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dismissible = TRUE
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)
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)
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shiny::fluidPage(
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title = title,
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server_ui,
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# shiny::uiOutput(ns("params_ui")),
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shiny::conditionalPanel(condition = "output.connect_success == true", params_ui, ns = ns),
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shiny::br()
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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$ns
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data_rv <- shiny::reactiveValues(
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dd_status = NULL,
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data_status = NULL,
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uri = NULL,
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project_name = NULL,
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info = NULL,
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arms = NULL,
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dd_list = NULL,
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data = NULL,
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rep_fields = NULL,
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code = NULL
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)
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shiny::observeEvent(list(input$api, input$uri), {
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shiny::req(input$api)
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shiny::req(input$uri)
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if (!is.null(input$uri)) {
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uri <- paste0(ifelse(
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endsWith(input$uri, "/"),
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input$uri,
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paste0(input$uri, "/")
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), "api/")
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} else {
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uri <- input$uri
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}
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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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shiny::observeEvent(list(input$data_connect), {
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shiny::req(input$api)
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shiny::req(data_rv$uri)
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parameters <- list(redcap_uri = data_rv$uri, token = input$api)
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# browser()
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shiny::withProgress({
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imported <- try(rlang::exec(REDCapR::redcap_metadata_read, !!!parameters),
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silent = TRUE)
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}, message = paste("Connecting to", data_rv$uri))
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## TODO: Simplify error messages
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if (inherits(imported, "try-error") ||
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NROW(imported) < 1 ||
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ifelse(is.list(imported), !isTRUE(imported$success), FALSE)) {
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if (ifelse(is.list(imported),
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!isTRUE(imported$success),
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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$info <- REDCapR::redcap_project_info_read(redcap_uri = data_rv$uri, token = input$api)$data
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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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see_data_text = i18n$t("Click to see data dictionary"),
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dataIdName = "see_dd",
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extra = tags$p(
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tags$b(
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phosphoricons::ph("check", weight = "bold"),
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i18n$t("Connected to server!")
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),
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glue::glue(
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i18n$t(
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"The {data_rv$info$project_title} project is loaded."
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)
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)
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),
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btn_show_data = TRUE
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)
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)
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data_rv$dd_list <- imported
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}
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}, ignoreInit = TRUE)
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}, warning = function(warn) {
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showNotification(paste0(warn), type = "warning")
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}, error = function(err) {
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showNotification(paste0(err), type = "err")
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})
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output$connect_success <- shiny::reactive(identical(data_rv$dd_status, "success"))
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shiny::outputOptions(output, "connect_success", suspendWhenHidden = FALSE)
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shiny::observeEvent(input$see_dd, {
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show_data(
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purrr::pluck(data_rv$dd_list, "data"),
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title = i18n$t("Data dictionary"),
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type = "modal",
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show_classes = FALSE,
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tags$b(i18n$t("Preview:"))
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)
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})
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shiny::observeEvent(input$see_data, {
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show_data(
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# purrr::pluck(data_rv$dd_list, "data"),
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data_rv$data,
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title = i18n$t("Imported data set"),
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type = "modal",
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show_classes = FALSE,
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tags$b(i18n$t("Preview:"))
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)
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})
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arms <- shiny::reactive({
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shiny::req(input$api)
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shiny::req(data_rv$uri)
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REDCapR::redcap_event_read(redcap_uri = data_rv$uri, token = input$api)$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 = i18n$t("Select fields/variables to import:"),
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choices = purrr::pluck(data_rv$dd_list, "data") |>
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dplyr::select(field_name, form_name) |>
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(\(.x) {
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split(.x$field_name, REDCapCAST::as_factor(.x$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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width = "100%"
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)
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})
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output$data_type <- shiny::renderUI({
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shiny::req(data_rv$info)
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if (isTRUE(data_rv$info$has_repeating_instruments_or_events)) {
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vectorSelectInput(
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inputId = ns("data_type"),
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label = i18n$t("Specify the data format"),
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choices = c(
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"Wide data (One row for each subject)" = "wide",
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"Long data for project with repeating instruments (default REDCap)" = "long"
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),
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selected = "wide",
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multiple = FALSE,
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width = "100%"
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)
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}
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})
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output$fill <- shiny::renderUI({
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shiny::req(data_rv$info)
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shiny::req(input$data_type)
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## Get repeated field
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data_rv$rep_fields <- data_rv$dd_list$data$field_name[data_rv$dd_list$data$form_name %in% repeated_instruments(uri = data_rv$uri, token = input$api)]
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if (input$data_type == "long" &&
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isTRUE(any(input$fields %in% data_rv$rep_fields))) {
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vectorSelectInput(
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inputId = ns("fill"),
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label = i18n$t("Fill missing values?"),
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choices = c(
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"Yes, fill missing, non-repeated values" = "yes",
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"No, leave the data as is" = "no"
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),
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selected = "no",
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multiple = FALSE,
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width = "100%"
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)
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}
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})
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shiny::observeEvent(input$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$arms <- shiny::renderUI({
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if (NROW(arms()) > 0) {
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vectorSelectInput(
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inputId = ns("arms"),
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selected = NULL,
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label = "Filter by events/arms",
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choices = stats::setNames(arms()[[3]], arms()[[1]]),
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multiple = TRUE,
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width = "100%"
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)
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}
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})
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shiny::observeEvent(input$data_import, {
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shiny::req(input$fields)
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# browser()
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record_id <- purrr::pluck(data_rv$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$filter,
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split_forms = ifelse(
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input$data_type == "long" && !is.null(input$data_type),
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"none",
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"all"
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)
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)
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shiny::withProgress(message = "Downloading REDCap data. Hold on for a moment..", {
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imported <- tryCatch(rlang::exec(REDCapCAST::read_redcap_tables, !!!parameters),
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silent = TRUE)
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})
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# d <- REDCapCAST::apply_factor_labels(data = imported$survey, meta = data_rv$dd_list$data)
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parameters_code <- parameters[c("uri",
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"fields",
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"events",
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"raw_or_label",
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"filter_logic")]
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code <- rlang::call2("easy_redcap",
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!!!utils::modifyList(
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parameters_code,
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list(
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data_format = ifelse(
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input$data_type == "long" && !is.null(input$data_type),
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"long",
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"wide"
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),
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project.name = simple_snake(data_rv$info$project_title)
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)
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),
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.ns = "REDCapCAST")
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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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data_rv$data_message <- imported$raw_text
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} else {
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data_rv$data_status <- "success"
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data_rv$data_message <- i18n$t("Requested data was retrieved!")
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## The data management below should be separated to allow for changing
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## "wide"/"long" without re-importing data
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if (parameters$split_form == "all") {
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out <- imported |>
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# redcap_wider()
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REDCapCAST::redcap_wider()
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} else {
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if (input$fill == "yes") {
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## Repeated fields
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## Non-repeated fields in current dataset
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inc_non_rep <- names(imported)[!names(imported) %in% data_rv$rep_fields]
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out <- imported |>
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drop_empty_event() |>
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dplyr::group_by(!!dplyr::sym(names(imported)[1])) |>
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tidyr::fill(inc_non_rep) |>
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dplyr::ungroup()
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} else {
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out <- imported |>
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drop_empty_event()
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}
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}
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## Ensure correct factor labels
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## It is a little hacky and should be included in the read_redcap_tables, but is lost along the way
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out <- REDCapCAST::apply_factor_labels(data = out, meta = data_rv$dd_list$data)
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in_data_check <- parameters$fields %in% names(out) |
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sapply(names(out), \(.x) any(sapply(
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parameters$fields, \(.y) startsWith(.x, .y)
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)))
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if (!any(in_data_check[-1])) {
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data_rv$data_status <- "warning"
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data_rv$data_message <- i18n$t(
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"Data retrieved, but it looks like only the ID was retrieved from the server. Please check with your REDCap administrator that you have required permissions for data access."
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)
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}
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if (!all(in_data_check)) {
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data_rv$data_status <- "warning"
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data_rv$data_message <- i18n$t(
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"Data retrieved, but it looks like not all requested fields were retrieved from the server. Please check with your REDCap administrator that you have required permissions for data access."
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)
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}
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data_rv$code <- code
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## Level labels nare lost at this point...
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data_rv$data <- out |>
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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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shiny::observeEvent(data_rv$data_status, {
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# browser()
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if (identical(data_rv$data_status, "error")) {
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datamods:::insert_error(mssg = data_rv$data_message,
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selector = ns("retrieved"))
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} else if (identical(data_rv$data_status, "success")) {
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datamods:::insert_alert(
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selector = ns("retrieved"),
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status = data_rv$data_status,
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# tags$p(
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# tags$b(phosphoricons::ph("check", weight = "bold"), "Success!"),
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# data_rv$data_message
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# ),
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include_data_alert(
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see_data_text = i18n$t("Click to see the imported data"),
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dataIdName = "see_data",
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extra = tags$p(tags$b(
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phosphoricons::ph("check", weight = "bold"),
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data_rv$data_message
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)),
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btn_show_data = TRUE
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)
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)
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} else {
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datamods:::insert_alert(
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selector = ns("retrieved"),
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status = data_rv$data_status,
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tags$p(
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tags$b(
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phosphoricons::ph("warning", weight = "bold"),
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"Warning!"
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),
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data_rv$data_message
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)
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)
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}
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})
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return(
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list(
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status = shiny::reactive(data_rv$data_status),
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name = shiny::reactive(data_rv$info$project_title),
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info = shiny::reactive(data_rv$info),
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code = shiny::reactive(data_rv$code),
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data = shiny::reactive(data_rv$data)
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)
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)
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}
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shiny::moduleServer(id = id, module = module)
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}
|
||
|
||
#' @importFrom htmltools tagList tags
|
||
#' @importFrom shiny icon getDefaultReactiveDomain
|
||
include_data_alert <- function(dataIdName = "see_data",
|
||
btn_show_data,
|
||
see_data_text = "Click to see data",
|
||
extra = NULL,
|
||
session = shiny::getDefaultReactiveDomain()) {
|
||
if (isTRUE(btn_show_data)) {
|
||
success_message <- tagList(extra,
|
||
tags$br(),
|
||
shiny::actionLink(
|
||
inputId = session$ns(dataIdName),
|
||
label = tagList(phosphoricons::ph("book-open-text"), see_data_text)
|
||
))
|
||
}
|
||
return(success_message)
|
||
}
|
||
|
||
# #' REDCap import teal data module
|
||
# #'
|
||
# #' @rdname redcap_read_shiny_module
|
||
# tdm_redcap_read <- teal::teal_data_module(
|
||
# ui <- function(id) {
|
||
# shiny::fluidPage(
|
||
# m_redcap_readUI(id)
|
||
# )
|
||
# },
|
||
# server = function(id) {
|
||
# m_redcap_readServer(id, output.format = "teal")
|
||
# }
|
||
# )
|
||
|
||
|
||
#' Test if url is valid format for REDCap API
|
||
#'
|
||
#' @param url url
|
||
#'
|
||
#' @returns logical
|
||
#' @export
|
||
#'
|
||
#' @examples
|
||
#' url <- c(
|
||
#' "www.example.com",
|
||
#' "redcap.your.inst/api/",
|
||
#' "https://redcap.your.inst/api/",
|
||
#' "https://your.inst/redcap/api/",
|
||
#' "https://www.your.inst/redcap/api/"
|
||
#' )
|
||
#' is_valid_redcap_url(url)
|
||
is_valid_redcap_url <- function(url) {
|
||
pattern <- "https://[^ /$.?#].[^\\s]*/api/$"
|
||
stringr::str_detect(url, pattern)
|
||
}
|
||
|
||
#' Validate REDCap token
|
||
#'
|
||
#' @param token token
|
||
#' @param pattern_env pattern
|
||
#'
|
||
#' @returns logical
|
||
#' @export
|
||
#'
|
||
#' @examples
|
||
#' token <- paste(sample(c(1:9, LETTERS[1:6]), 32, TRUE), collapse = "")
|
||
#' is_valid_token(token)
|
||
is_valid_token <- function(token,
|
||
pattern_env = NULL,
|
||
nchar = 32) {
|
||
checkmate::assert_character(token, any.missing = TRUE, len = 1)
|
||
|
||
if (!is.null(pattern_env)) {
|
||
checkmate::assert_character(pattern_env, any.missing = FALSE, len = 1)
|
||
pattern <- pattern_env
|
||
} else {
|
||
pattern <- glue::glue("^([0-9A-Fa-f]{<nchar>})(?:\\n)?$",
|
||
.open = "<",
|
||
.close = ">")
|
||
}
|
||
|
||
if (is.na(token)) {
|
||
out <- FALSE
|
||
} else if (is.null(token)) {
|
||
out <- FALSE
|
||
} else if (nchar(token) == 0L) {
|
||
out <- FALSE
|
||
} else if (!grepl(pattern, token, perl = TRUE)) {
|
||
out <- FALSE
|
||
} else {
|
||
out <- TRUE
|
||
}
|
||
out
|
||
}
|
||
|
||
#' Get names of repeated instruments
|
||
#'
|
||
#' @param uri REDCap database uri
|
||
#' @param token database token
|
||
#'
|
||
#' @returns vector
|
||
#' @export
|
||
#'
|
||
repeated_instruments <- function(uri, token) {
|
||
instruments <- REDCapR::redcap_event_instruments(redcap_uri = uri, token = token)
|
||
unique(instruments$data$form[duplicated(instruments$data$form)])
|
||
}
|
||
|
||
#' Drop empty events from REDCap export
|
||
#'
|
||
#' @param data data
|
||
#' @param event "redcap_event_name", "redcap_repeat_instrument" or
|
||
#' "redcap_repeat_instance"
|
||
#'
|
||
#' @returns data.frame
|
||
#' @export
|
||
#'
|
||
drop_empty_event <- function(data, event = "redcap_event_name") {
|
||
generics <- c(
|
||
names(data)[1],
|
||
"redcap_event_name",
|
||
"redcap_repeat_instrument",
|
||
"redcap_repeat_instance"
|
||
)
|
||
|
||
filt <- split(data, data[[event]]) |>
|
||
lapply(\(.x) {
|
||
dplyr::select(.x, -tidyselect::all_of(generics)) |>
|
||
REDCapCAST::all_na()
|
||
}) |>
|
||
unlist()
|
||
|
||
data[data[[event]] %in% names(filt)[!filt], ]
|
||
}
|
||
|
||
|
||
#' Test app for the redcap_read_shiny_module
|
||
#'
|
||
#' @rdname redcap_read_shiny_module
|
||
#'
|
||
#' @examples
|
||
#' \dontrun{
|
||
#' redcap_demo_app()
|
||
#' }
|
||
redcap_demo_app <- function() {
|
||
ui <- shiny::fluidPage(
|
||
m_redcap_readUI("data", url = NULL),
|
||
DT::DTOutput("data"),
|
||
shiny::tags$b("Code:"),
|
||
shiny::verbatimTextOutput(outputId = "code")
|
||
)
|
||
server <- function(input, output, session) {
|
||
data_val <- m_redcap_readServer(id = "data")
|
||
|
||
output$data <- DT::renderDataTable({
|
||
shiny::req(data_val$data)
|
||
data_val$data()
|
||
}, options = list(scrollX = TRUE, pageLength = 5), )
|
||
output$code <- shiny::renderPrint({
|
||
shiny::req(data_val$code)
|
||
data_val$code()
|
||
})
|
||
}
|
||
shiny::shinyApp(ui, server)
|
||
}
|